1
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Mohan M, Demerdash ON, Simmons BA, Singh S, Kidder MK, Smith JC. Physics-Based Machine Learning Models Predict Carbon Dioxide Solubility in Chemically Reactive Deep Eutectic Solvents. ACS Omega 2024; 9:19548-19559. [PMID: 38708262 PMCID: PMC11064036 DOI: 10.1021/acsomega.4c01175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/25/2024] [Accepted: 04/03/2024] [Indexed: 05/07/2024]
Abstract
Carbon dioxide (CO2) is a detrimental greenhouse gas and is the main contributor to global warming. In addressing this environmental challenge, a promising approach emerges through the utilization of deep eutectic solvents (DESs) as an ecofriendly and sustainable medium for effective CO2 capture. Chemically reactive DESs, which form chemical bonds with the CO2, are superior to nonreactive, physically based DESs for CO2 absorption. However, there are no accurate computational models that provide accurate predictions of the CO2 solubility in chemically reactive DESs. Here, we develop machine learning (ML) models to predict the solubility of CO2 in chemically reactive DESs. As training data, we collected 214 data points for the CO2 solubility in 149 different chemically reactive DESs at different temperatures, pressures, and DES molar ratios from published work. The physics-driven input features for the ML models include σ-profile descriptors that quantify the relative probability of a molecular surface segment having a certain screening charge density and were calculated with the first-principle quantum chemical method COSMO-RS. We show here that, although COSMO-RS does not explicitly calculate chemical reaction profiles, the COSMO-RS-derived σ-profile features can be used to predict bond formation. Of the models trained, an artificial neural network (ANN) provides the most accurate CO2 solubility prediction with an average absolute relative deviation of 2.94% on the testing sets. Overall, this work provides ML models that can predict CO2 solubility precisely and thus accelerate the design and application of chemically reactive DESs.
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Affiliation(s)
- Mood Mohan
- Biosciences
Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Omar N. Demerdash
- Biosciences
Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Blake A. Simmons
- Deconstruction
Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
- Biological
Systems and Engineering Division, Lawrence
Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Seema Singh
- Deconstruction
Division, Joint BioEnergy Institute, 5885 Hollis Street, Emeryville, California 94608, United States
| | - Michelle K. Kidder
- Manufacturing
Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States
| | - Jeremy C. Smith
- Biosciences
Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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2
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Smith MD, Darryl Quarles L, Demerdash O, Smith JC. Drugging the entire human proteome: Are we there yet? Drug Discov Today 2024; 29:103891. [PMID: 38246414 DOI: 10.1016/j.drudis.2024.103891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 01/23/2024]
Abstract
Each of the ∼20,000 proteins in the human proteome is a potential target for compounds that bind to it and modify its function. The 3D structures of most of these proteins are now available. Here, we discuss the prospects for using these structures to perform proteome-wide virtual HTS (VHTS). We compare physics-based (docking) and AI VHTS approaches, some of which are now being applied with large databases of compounds to thousands of targets. Although preliminary proteome-wide screens are now within our grasp, further methodological developments are expected to improve the accuracy of the results.
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Affiliation(s)
- Micholas Dean Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - L Darryl Quarles
- Departments of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; ORRxD LLC, 3404 Olney Drive, Durham, NC 27705, USA
| | - Omar Demerdash
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, Oak Ridge, TN 37830, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA.
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3
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Mohan M, Jetti KD, Smith MD, Demerdash ON, Kidder MK, Smith JC. Accurate Machine Learning for Predicting the Viscosities of Deep Eutectic Solvents. J Chem Theory Comput 2024. [PMID: 38387055 DOI: 10.1021/acs.jctc.3c01163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2024]
Abstract
Deep eutectic solvents (DESs) are emerging as environmentally friendly designer solvents for mass transport and heat transfer processes in industrial applications; however, the lack of accurate tools to predict and thus control their viscosities under both a range of environmental factors and formulations hinders their general application. While DESs may serve as designer solvents, with nearly unlimited combinations, this unfortunately makes it experimentally infeasible to comprehensively measure the viscosities of all DESs of potential industrial interest. To assist in the design of DESs, we have developed several new machine learning (ML) models that accurately and rapidly predict the viscosities of a diverse group of DESs at different temperatures and molar ratios using, to date, one of the most comprehensive data sets containing the properties of over 670 DESs over a wide range of temperatures (278.15-385.25 K). Three ML models, including support vector regression (SVR), feed forward neural networks (FFNNs), and categorical boosting (CatBoost), were developed to predict DES viscosity as a function of temperature and molar ratio and contrasted with multilinear and two-factor polynomial regression baselines. Quantum chemistry-based, COSMO-RS-derived sigma profile (σ-profile) features were used as inputs for the ML models. The CatBoost model is excellent at externally predicting DES viscosity, as indicated by high R2 (0.99) and low root-mean-square-error (RMSE) and average absolute relative deviations (AARD) (5.22%) values for the testing data sets, and 98% of the data points lie within the 15% of AARD deviations. Furthermore, SHapley additive explanation (SHAP) analysis was employed to interpret the ML results and rationalize the viscosity predictions. The result is an ML approach that accurately predicts viscosity and will aid in accelerating the design of appropriate DESs for industrial applications.
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Affiliation(s)
- Mood Mohan
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Karuna Devi Jetti
- Department of Biotechnology, GIS, GITAM,Vishakhapatnam, Andhra Pradesh 530045, India
| | - Micholas Dean Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Omar N Demerdash
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Michelle K Kidder
- Manufacturing Science Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, United States
| | - Jeremy C Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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4
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Sethuraman V, Vermaas JV, Liang L, Ragauskas AJ, Smith JC, Petridis L. Atomistic Simulations of Polydisperse Lignin Melts Using Simple Polydisperse Residue Input Generator. Biomacromolecules 2024; 25:767-777. [PMID: 38157547 DOI: 10.1021/acs.biomac.3c00951] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Understanding the physics of lignin will help rationalize its function in plant cell walls as well as aiding practical applications such as deriving biofuels and bioproducts. Here, we present SPRIG (Simple Polydisperse Residue Input Generator), a program for generating atomic-detail models of random polydisperse lignin copolymer melts i.e., the state most commonly found in nature. Using these models, we use all-atom molecular dynamics (MD) simulations to investigate the conformational and dynamic properties of polydisperse melts representative of switchgrass (Panicum virgatum L.) lignin. Polydispersity, branching and monolignol sequence are found to not affect the calculated glass transition temperature, Tg. The Flory-Huggins scaling parameter for the segmental radius of gyration is 0.42 ± 0.02, indicating that the chains exhibit statistics that lie between a globular chain and an ideal Gaussian chain. Below Tg the atomic mean squared displacements are independent of molecular weight. In contrast, above Tg, they decrease with increasing molecular weight. Therefore, a monodisperse lignin melt is a good approximation to this polydisperse lignin when only static properties are probed, whereas the molecular weight distribution needs to be considered while analyzing lignin dynamics.
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Affiliation(s)
- Vaidyanathan Sethuraman
- Center for Molecular Biophysics, Oak Ridge National Laboratory, 1-Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Josh V Vermaas
- MSU-DOE Plant Research Laboratory and Department of Biochemistry and Molecular Biology, Michigan State University, 612 Wilson Road, East Lansing, Michigan 48824, United States
| | - Luna Liang
- Department of Chemical & Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
| | - Arthur J Ragauskas
- Department of Chemical & Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee 37996, United States
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, Tennessee 37996, United States
- UTK-ORNL Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics, Oak Ridge National Laboratory, 1-Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Loukas Petridis
- Center for Molecular Biophysics, Oak Ridge National Laboratory, 1-Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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Agarwal R, T RR, Smith JC. Comparative Assessment of Pose Prediction Accuracy in RNA-Ligand Docking. J Chem Inf Model 2023; 63:7444-7452. [PMID: 37972310 DOI: 10.1021/acs.jcim.3c01533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2023]
Abstract
Structure-based virtual high-throughput screening is used in early-stage drug discovery. Over the years, docking protocols and scoring functions for protein-ligand complexes have evolved to improve the accuracy in the computation of binding strengths and poses. In the past decade, RNA has also emerged as a target class for new small-molecule drugs. However, most ligand docking programs have been validated and tested for proteins and not RNA. Here, we test the docking power (pose prediction accuracy) of three state-of-the-art docking protocols on 173 RNA-small molecule crystal structures. The programs are AutoDock4 (AD4) and AutoDock Vina (Vina), which were designed for protein targets, and rDock, which was designed for both protein and nucleic acid targets. AD4 performed relatively poorly. For RNA targets for which a crystal structure of a bound ligand used to limit the docking search space is available and for which the goal is to identify new molecules for the same pocket, rDock performs slightly better than Vina, with success rates of 48% and 63%, respectively. However, in the more common type of early-stage drug discovery setting, in which no structure of a ligand-target complex is known and for which a larger search space is defined, rDock performed similarly to Vina, with a low success rate of ∼27%. Vina was found to have bias for ligands with certain physicochemical properties, whereas rDock performs similarly for all ligand properties. Thus, for projects where no ligand-protein structure already exists, Vina and rDock are both applicable. However, the relatively poor performance of all methods relative to protein-target docking illustrates a need for further methods refinement.
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Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Rajitha Rajeshwar T
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996-1939, United States
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Misra G, Rajawat J, Pal R, Smith JC, Kumar A. Targeted inhibition of MASTL kinase activity induces apoptosis in breast cancer. Life Sci 2023; 334:122250. [PMID: 37931742 DOI: 10.1016/j.lfs.2023.122250] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/20/2023] [Accepted: 11/03/2023] [Indexed: 11/08/2023]
Abstract
Microtubule-associated serine/threonine kinase-like (MASTL) (or Greatwall kinase (GWL)) is an important cell cycle regulating kinase that regulates the G2-M transition. Uncontrolled MASTL activity is implicated in breast cancer progression. To date, very few inhibitors have been reported against this protein. Here, structure-based computational modeling indicates that the natural product flavopiridol (FLV) binds strongly to MASTL and these results are validated using molecular dynamics simulation studies. An in vitro kinase assay reveals an EC50 (effective concentration) value of FLV to be 82.1 nM and a better IC50 compared to the positive reference compound, staurosporine. FLV is found to inhibit MASTL kinase activity, arresting the cell growth in the G1 phase and inducing apoptosis in breast cancer cells. Consistent with these results differential gene expression obtained using RNA sequencing studies, and validated by RT PCR and immunoblot analysis, indicate that MASTL inhibition induces cell cycle arrest and apoptotic-related genes. Furthermore, metastasis- and inflammation-related genes are downregulated. Thus, the deregulation of MASTL signaling pathways on targeted inhibition of its kinase activity is revealed. This study lays a strong foundation for investigating FLV as a lead compound in breast cancer therapeutics.
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Affiliation(s)
- Gauri Misra
- National Institute of Biologicals (Ministry of Health and Family Welfare, Government of India), Noida 201309, India.
| | - Jyotika Rajawat
- Institute of Advanced Molecular Genetics & Infectious Diseases, ONGC, Centre for Advanced Studies, University of Lucknow, Lucknow 226 007, UP, India
| | - Rajesh Pal
- Precision Sarcoma Research Group, German Cancer Research Centre (DKFZ), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Amit Kumar
- Department of Electrical and Electronic Engineering, University of Cagliari, Via Marengo 2, 09123 Cagliari, Italy
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7
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Liu SH, Xiao Z, Smith JC, Quarles LD. Structural asymmetry in FGF23 signaling. Trends Pharmacol Sci 2023; 44:862-864. [PMID: 37778940 DOI: 10.1016/j.tips.2023.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 09/19/2023] [Accepted: 09/19/2023] [Indexed: 10/03/2023]
Abstract
Chen et al. have derived cryogenic electron microscopy (cryo-EM) structures of signaling complexes of the endocrine hormone fibroblast growth factor 23 (FGF23) with fibroblast growth factor receptor (FGFR), α-Klotho, and heparin sulfate. These structures are asymmetric, leading to questions concerning in vivo function, and will facilitate structure-based drug design to modulate FGF23 signaling.
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Affiliation(s)
- Shih-Hsien Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - Zhousheng Xiao
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, USA
| | - L Darryl Quarles
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA.
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8
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Vural D, Shrestha UR, Petridis L, Smith JC. Water molecule ordering on the surface of an intrinsically disordered protein. Biophys J 2023; 122:4326-4335. [PMID: 37838830 PMCID: PMC10722392 DOI: 10.1016/j.bpj.2023.10.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/26/2023] [Accepted: 10/10/2023] [Indexed: 10/16/2023] Open
Abstract
The dynamics and local structure of the hydration water on surfaces of folded proteins have been extensively investigated. However, our knowledge of the hydration of intrinsically disordered proteins (IDPs) is more limited. Here, we compare the local structure of water molecules hydrating a globular protein, lysozyme, and the intrinsically disordered N-terminal of c-Src kinase (SH4UD) using molecular dynamics simulation. The radial distributions from the protein surface of the first and the second hydration shells are similar for the folded protein and the IDP. However, water molecules in the first hydration shell of both the folded protein and the IDP are perturbed from the bulk. This perturbation involves a loss of tetrahedrality, which is, however, significantly more marked for the folded protein than the IDP. This difference arises from an increase in the first hydration shell of the IDP of the fraction of hydration water molecules interacting with oxygen. The water ordering is independent of the compactness of the IDP. In contrast, the lifetimes of water molecules in the first hydration shell increase with IDP compactness, indicating a significant impact of IDP configuration on water surface pocket kinetics, which here is linked to differential pocket volumes and polarities.
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Affiliation(s)
- Derya Vural
- Department of Physics, Marmara University, Istanbul, Türkiye; Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee.
| | - Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, Tennessee; Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
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Xiao Z, Cao L, Smith MD, Li H, Li W, Smith JC, Quarles LD. Genetic interactions between polycystin-1 and Wwtr1 in osteoblasts define a novel mechanosensing mechanism regulating bone formation in mice. Bone Res 2023; 11:57. [PMID: 37884491 PMCID: PMC10603112 DOI: 10.1038/s41413-023-00295-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 08/30/2023] [Accepted: 09/18/2023] [Indexed: 10/28/2023] Open
Abstract
Molecular mechanisms transducing physical forces in the bone microenvironment to regulate bone mass are poorly understood. Here, we used mouse genetics, mechanical loading, and pharmacological approaches to test the possibility that polycystin-1 and Wwtr1 have interdependent mechanosensing functions in osteoblasts. We created and compared the skeletal phenotypes of control Pkd1flox/+;Wwtr1flox/+, Pkd1Oc-cKO, Wwtr1Oc-cKO, and Pkd1/Wwtr1Oc-cKO mice to investigate genetic interactions. Consistent with an interaction between polycystins and Wwtr1 in bone in vivo, Pkd1/Wwtr1Oc-cKO mice exhibited greater reductions of BMD and periosteal MAR than either Wwtr1Oc-cKO or Pkd1Oc-cKO mice. Micro-CT 3D image analysis indicated that the reduction in bone mass was due to greater loss in both trabecular bone volume and cortical bone thickness in Pkd1/Wwtr1Oc-cKO mice compared to either Pkd1Oc-cKO or Wwtr1Oc-cKO mice. Pkd1/Wwtr1Oc-cKO mice also displayed additive reductions in mechanosensing and osteogenic gene expression profiles in bone compared to Pkd1Oc-cKO or Wwtr1Oc-cKO mice. Moreover, we found that Pkd1/Wwtr1Oc-cKO mice exhibited impaired responses to tibia mechanical loading in vivo and attenuation of load-induced mechanosensing gene expression compared to control mice. Finally, control mice treated with a small molecule mechanomimetic, MS2 that activates the polycystin complex resulted in marked increases in femoral BMD and periosteal MAR compared to vehicle control. In contrast, Pkd1/Wwtr1Oc-cKO mice were resistant to the anabolic effects of MS2. These findings suggest that PC1 and Wwtr1 form an anabolic mechanotransduction signaling complex that mediates mechanical loading responses and serves as a potential novel therapeutic target for treating osteoporosis.
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Affiliation(s)
- Zhousheng Xiao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA.
| | - Li Cao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Micholas Dean Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee-Knoxville, Knoxville, TN, 37996-1939, USA
| | - Hanxuan Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Wei Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee-Knoxville, Knoxville, TN, 37996-1939, USA
| | - Leigh Darryl Quarles
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
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Dale JB, Aranha MP, Penfound TA, Salehi S, Smith JC. Structure-guided design of a broadly cross-reactive multivalent group a streptococcal vaccine. Vaccine 2023; 41:5841-5847. [PMID: 37596198 PMCID: PMC10529471 DOI: 10.1016/j.vaccine.2023.08.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 08/09/2023] [Accepted: 08/11/2023] [Indexed: 08/20/2023]
Abstract
The M protein of group A streptococci (Strep A) is a major virulence determinant and protective antigen. The N-terminal region of the M protein is variable in sequence, defines the M/emm type, and contains epitopes that elicit opsonic antibodies that protect animals from challenge infections. Although there are >200 M types of Strep A, there is now evidence that structurally related M proteins can be grouped into clusters and that immunity may be cluster-specific in addition to M type-specific. This observation has led to recent studies of structure-based design of multivalent M peptide vaccines to select peptides predicted to cross-react with heterologous M types to improve vaccine coverage. In the current study, we have applied a refined series of peptide structural algorithms to predict immunological cross-reactivity among 117 N-terminal M peptides representing the most prevalent M types of Strep A. Based on the results of the structural analyses, in combination with global M type prevalence data, we constructed a 32-valent vaccine containing 19 cross-reactive vaccine candidates predicted to cross-react with 37 heterologous M peptides to which were added 13 type-specific M peptides. The 4-protein recombinant vaccine was immunogenic in rabbits and elicited significant levels of antibodies against 31/32 (97%) vaccine peptides and 28/37 (76%) peptides predicted to cross-react. The vaccine antisera also promoted opsonophagocytic killing of vaccine and cross-reactive M types of Strep A. Based on a recent analysis of M type prevalence of Strep A, the potential global coverage of the 32-valent vaccine is ∼90%, ranging from 68% in Africa to 95% in North America. Our results indicate the utility of structure-based design that may be applied to future studies of broadly protective M peptide vaccines.
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Affiliation(s)
- James B Dale
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States; Department of Microbiology, Immunology, and Biochemistry, University of Tennessee Health Science Center, Memphis, TN 38163, United States.
| | - Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Thomas A Penfound
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Sanaz Salehi
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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11
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Mohan M, Smith MD, Demerdash O, Kidder MK, Smith JC. Predictive understanding of the surface tension and velocity of sound in ionic liquids using machine learning. J Chem Phys 2023; 158:2893752. [PMID: 37260016 DOI: 10.1063/5.0147052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Accepted: 05/12/2023] [Indexed: 06/02/2023] Open
Abstract
Knowledge of the physical properties of ionic liquids (ILs), such as the surface tension and speed of sound, is important for both industrial and research applications. Unfortunately, technical challenges and costs limit exhaustive experimental screening efforts of ILs for these critical properties. Previous work has demonstrated that the use of quantum-mechanics-based thermochemical property prediction tools, such as the conductor-like screening model for real solvents, when combined with machine learning (ML) approaches, may provide an alternative pathway to guide the rapid screening and design of ILs for desired physiochemical properties. However, the question of which machine-learning approaches are most appropriate remains. In the present study, we examine how different ML architectures, ranging from tree-based approaches to feed-forward artificial neural networks, perform in generating nonlinear multivariate quantitative structure-property relationship models for the prediction of the temperature- and pressure-dependent surface tension of and speed of sound in ILs over a wide range of surface tensions (16.9-76.2 mN/m) and speeds of sound (1009.7-1992 m/s). The ML models are further interrogated using the powerful interpretation method, shapley additive explanations. We find that several different ML models provide high accuracy, according to traditional statistical metrics. The decision tree-based approaches appear to be the most accurate and precise, with extreme gradient-boosting trees and gradient-boosting trees being the best performers. However, our results also indicate that the promise of using machine-learning to gain deep insights into the underlying physics driving structure-property relationships in ILs may still be somewhat premature.
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Affiliation(s)
- Mood Mohan
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Micholas Dean Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Omar Demerdash
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Michelle K Kidder
- Energy Science and Technology Directorate, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6201, USA
| | - Jeremy C Smith
- Biosciences Division and Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
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12
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nath D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Author Correction: Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2023; 13:8918. [PMID: 37264107 DOI: 10.1038/s41598-023-35960-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nath
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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13
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Xiao Z, Cao L, Smith MD, Li H, Li W, Smith JC, Quarles LD. Genetic interactions between Polycystin-1 and TAZ in osteoblasts define a novel mechanosensing mechanism regulating bone formation in mice. Res Sq 2023:rs.3.rs-2957026. [PMID: 37398127 PMCID: PMC10312920 DOI: 10.21203/rs.3.rs-2957026/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Molecular mechanisms transducing physical forces in the bone microenvironment to regulate bone mass are poorly understood. Here, we used mouse genetics, mechanical loading, and pharmacological approaches to test the possibility that polycystin-1 and TAZ have interdependent mechanosensing functions in osteoblasts. We created and compared the skeletal phenotypes of control Pkd1flox/+;TAZflox/+, single Pkd1Oc-cKO, single TAZOc-cKO, and double Pkd1/TAZOc-cKO mice to investigate genetic interactions. Consistent with an interaction between polycystins and TAZ in bone in vivo, double Pkd1/TAZOc-cKO mice exhibited greater reductions of BMD and periosteal MAR than either single TAZOc-cKO or Pkd1Oc-cKO mice. Micro-CT 3D image analysis indicated that the reduction in bone mass was due to greater loss in both trabecular bone volume and cortical bone thickness in double Pkd1/TAZOc-cKO mice compared to either single Pkd1Oc-cKO or TAZOc-cKO mice. Double Pkd1/TAZOc-cKO mice also displayed additive reductions in mechanosensing and osteogenic gene expression profiles in bone compared to single Pkd1Oc-cKO or TAZOc-cKO mice. Moreover, we found that double Pkd1/TAZOc-cKO mice exhibited impaired responses to tibia mechanical loading in vivo and attenuation of load-induced mechanosensing gene expression compared to control mice. Finally, control mice treated with a small molecule mechanomimetic MS2 had marked increases in femoral BMD and periosteal MAR compared to vehicle control. In contrast, double Pkd1/TAZOc-cKO mice were resistant to the anabolic effects of MS2 that activates the polycystin signaling complex. These findings suggest that PC1 and TAZ form an anabolic mechanotransduction signaling complex that responds to mechanical loading and serve as a potential novel therapeutic target for treating osteoporosis.
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Affiliation(s)
- Zhousheng Xiao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163
| | - Li Cao
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163
| | - Micholas Dean Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee-Knoxville, Knoxville, TN, 37996-1939
| | - Hanxuan Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163
| | - Wei Li
- Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN, 38163
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee-Knoxville, Knoxville, TN, 37996-1939
| | - Leigh Darryl Quarles
- Department of Medicine, University of Tennessee Health Science Center, Memphis, TN, 38163
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14
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Shen Y, Parks JM, Smith JC. HLA-Clus: HLA class I clustering based on 3D structure. BMC Bioinformatics 2023; 24:189. [PMID: 37161375 PMCID: PMC10169335 DOI: 10.1186/s12859-023-05297-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 04/18/2023] [Indexed: 05/11/2023] Open
Abstract
BACKGROUND In a previous paper, we classified populated HLA class I alleles into supertypes and subtypes based on the similarity of 3D landscape of peptide binding grooves, using newly defined structure distance metric and hierarchical clustering approach. Compared to other approaches, our method achieves higher correlation with peptide binding specificity, intra-cluster similarity (cohesion), and robustness. Here we introduce HLA-Clus, a Python package for clustering HLA Class I alleles using the method we developed recently and describe additional features including a new nearest neighbor clustering method that facilitates clustering based on user-defined criteria. RESULTS The HLA-Clus pipeline includes three stages: First, HLA Class I structural models are coarse grained and transformed into clouds of labeled points. Second, similarities between alleles are determined using a newly defined structure distance metric that accounts for spatial and physicochemical similarities. Finally, alleles are clustered via hierarchical or nearest-neighbor approaches. We also interfaced HLA-Clus with the peptide:HLA affinity predictor MHCnuggets. By using the nearest neighbor clustering method to select optimal allele-specific deep learning models in MHCnuggets, the average accuracy of peptide binding prediction of rare alleles was improved. CONCLUSIONS The HLA-Clus package offers a solution for characterizing the peptide binding specificities of a large number of HLA alleles. This method can be applied in HLA functional studies, such as the development of peptide affinity predictors, disease association studies, and HLA matching for grafting. HLA-Clus is freely available at our GitHub repository ( https://github.com/yshen25/HLA-Clus ).
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Affiliation(s)
- Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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15
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Hicks A, Abraham P, Leite W, Zhang Q, Weiss KL, O'Neill H, Petridis L, Smith JC. SCOMAP-XD: atomistic deuterium contrast matching for small-angle neutron scattering in biology. Acta Crystallogr D Struct Biol 2023; 79:420-434. [PMID: 37092970 DOI: 10.1107/s2059798323002899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/27/2023] [Indexed: 04/25/2023] Open
Abstract
The contrast-variation method in small-angle neutron scattering (SANS) is a uniquely powerful technique for determining the structure of individual components in biomolecular systems containing regions of different neutron scattering length density ρ. By altering the ρ of the target solute and the solvent through judicious incorporation of deuterium, the scattering of desired solute features can be highlighted. Most contrast-variation methods focus on highlighting specific bulk solute elements, but not on how the scattering at specific scattering vectors q, which are associated with specific structural distances, changes with contrast. Indeed, many systems exhibit q-dependent contrast effects. Here, a method is presented for calculating both bulk contrast-match points and q-dependent contrast using 3D models with explicit solute and solvent atoms and SASSENA, an explicit-atom SANS calculator. The method calculates the bulk contrast-match points within 2.4% solvent D2O accuracy for test protein-nucleic acid and lipid nanodisc systems. The method incorporates a general model for the incorporation of deuterium at non-exchangeable sites that was derived by performing mass spectrometry on green fluorescent protein. The method also decomposes the scattering profile into its component parts and identifies structural features that change with contrast. The method is readily applicable to a variety of systems, will expand the understanding of q-dependent contrast matching and will aid in the optimization of next-generation neutron scattering experiments.
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Affiliation(s)
- Alan Hicks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Paul Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Wellington Leite
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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16
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Rogers DM, Agarwal R, Vermaas JV, Smith MD, Rajeshwar RT, Cooper C, Sedova A, Boehm S, Baker M, Glaser J, Smith JC. SARS-CoV2 billion-compound docking. Sci Data 2023; 10:173. [PMID: 36977690 PMCID: PMC10044124 DOI: 10.1038/s41597-023-01984-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 01/24/2023] [Indexed: 03/30/2023] Open
Abstract
This dataset contains ligand conformations and docking scores for 1.4 billion molecules docked against 6 structural targets from SARS-CoV2, representing 5 unique proteins: MPro, NSP15, PLPro, RDRP, and the Spike protein. Docking was carried out using the AutoDock-GPU platform on the Summit supercomputer and Google Cloud. The docking procedure employed the Solis Wets search method to generate 20 independent ligand binding poses per compound. Each compound geometry was scored using the AutoDock free energy estimate, and rescored using RFScore v3 and DUD-E machine-learned rescoring models. Input protein structures are included, suitable for use by AutoDock-GPU and other docking programs. As the result of an exceptionally large docking campaign, this dataset represents a valuable resource for discovering trends across small molecule and protein binding sites, training AI models, and comparing to inhibitor compounds targeting SARS-CoV-2. The work also gives an example of how to organize and process data from ultra-large docking screens.
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Affiliation(s)
- David M Rogers
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
| | - Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Josh V Vermaas
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Micholas Dean Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Rajitha T Rajeshwar
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA
| | - Connor Cooper
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Biological Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Ada Sedova
- Biological Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Swen Boehm
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Matthew Baker
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jens Glaser
- Computing and Computational Sciences Directorate, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee, Knoxville, Knoxville, TN, 37996, USA.
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17
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Taylor MK, Williams EP, Xue Y, Jenjaroenpun P, Wongsurawat T, Smith AP, Smith AM, Parvathareddy J, Kong Y, Vogel P, Cao X, Reichard W, Spruill-Harrell B, Samarasinghe AE, Nookaew I, Fitzpatrick EA, Smith MD, Aranha M, Smith JC, Jonsson CB. Dissecting Phenotype from Genotype with Clinical Isolates of SARS-CoV-2 First Wave Variants. Viruses 2023; 15:611. [PMID: 36992320 PMCID: PMC10059853 DOI: 10.3390/v15030611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 02/06/2023] [Accepted: 02/10/2023] [Indexed: 02/25/2023] Open
Abstract
The emergence and availability of closely related clinical isolates of SARS-CoV-2 offers a unique opportunity to identify novel nonsynonymous mutations that may impact phenotype. Global sequencing efforts show that SARS-CoV-2 variants have emerged and then been replaced since the beginning of the pandemic, yet we have limited information regarding the breadth of variant-specific host responses. Using primary cell cultures and the K18-hACE2 mouse, we investigated the replication, innate immune response, and pathology of closely related, clinical variants circulating during the first wave of the pandemic. Mathematical modeling of the lung viral replication of four clinical isolates showed a dichotomy between two B.1. isolates with significantly faster and slower infected cell clearance rates, respectively. While isolates induced several common immune host responses to infection, one B.1 isolate was unique in the promotion of eosinophil-associated proteins IL-5 and CCL11. Moreover, its mortality rate was significantly slower. Lung microscopic histopathology suggested further phenotypic divergence among the five isolates showing three distinct sets of phenotypes: (i) consolidation, alveolar hemorrhage, and inflammation, (ii) interstitial inflammation/septal thickening and peribronchiolar/perivascular lymphoid cells, and (iii) consolidation, alveolar involvement, and endothelial hypertrophy/margination. Together these findings show divergence in the phenotypic outcomes of these clinical isolates and reveal the potential importance of nonsynonymous mutations in nsp2 and ORF8.
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Affiliation(s)
- Mariah K. Taylor
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Evan P. Williams
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Yi Xue
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Piroon Jenjaroenpun
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Thidathip Wongsurawat
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Amanda P. Smith
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Amber M. Smith
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Jyothi Parvathareddy
- Regional Biocontainment Laboratory, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ying Kong
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Peter Vogel
- Veterinary Pathology Core Laboratory, St Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Xueyuan Cao
- Department of Health Promotion and Disease Prevention, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Walter Reichard
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Briana Spruill-Harrell
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Amali E. Samarasinghe
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Department of Pediatrics, The University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | - Intawat Nookaew
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Elizabeth A. Fitzpatrick
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Micholas Dean Smith
- Center for Molecular Biophysics, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Michelle Aranha
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Jeremy C. Smith
- Center for Molecular Biophysics, University of Tennessee-Oak Ridge National Laboratory, Knoxville, TN 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, The University of Tennessee- Knoxville, Knoxville, TN 37996, USA
| | - Colleen B. Jonsson
- Department of Microbiology, Immunology and Biochemistry, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Institute for the Study of Host-Pathogen Systems, University of Tennessee Health Science Center, Memphis, TN 38163, USA
- Regional Biocontainment Laboratory, The University of Tennessee Health Science Center, Memphis, TN 38163, USA
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18
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Gurumoorthy V, Shrestha UR, Zhang Q, Pingali SV, Boder ET, Urban VS, Smith JC, Petridis L, O'Neill H. Disordered Domain Shifts the Conformational Ensemble of the Folded Regulatory Domain of the Multidomain Oncoprotein c-Src. Biomacromolecules 2023; 24:714-723. [PMID: 36692364 DOI: 10.1021/acs.biomac.2c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
c-Src kinase is a multidomain non-receptor tyrosine kinase that aberrantly phosphorylates several signaling proteins in cancers. Although the structural properties of the regulatory domains (SH3-SH2) and the catalytic kinase domain have been extensively characterized, there is less knowledge about the N-terminal disordered region (SH4UD) and its interactions with the other c-Src domains. Here, we used domain-selective isotopic labeling combined with the small-angle neutron scattering contrast matching technique to study SH4UD interactions with SH3-SH2. Our results show that in the presence of SH4UD, the radius of gyration (Rg) of SH3-SH2 increases, indicating that it has a more extended conformation. Hamiltonian replica exchange molecular dynamics simulations provide a detailed molecular description of the structural changes in SH4UD-SH3-SH2 and show that the regulatory loops of SH3 undergo significant conformational changes in the presence of SH4UD, while SH2 remains largely unchanged. Overall, this study highlights how a disordered region can drive a folded region of a multidomain protein to become flexible, which may be important for allosteric interactions with binding partners. This may help in the design of therapeutic interventions that target the regulatory domains of this important family of kinases.
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Affiliation(s)
- Viswanathan Gurumoorthy
- UT/ORNL Graduate School of Genome and Science Technology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Utsab R Shrestha
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Qiu Zhang
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sai Venkatesh Pingali
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Eric T Boder
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Volker S Urban
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Hugh O'Neill
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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19
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Agarwal R, Smith JC. Speed vs Accuracy: Effect on Ligand Pose Accuracy of Varying Box Size and Exhaustiveness in AutoDock Vina. Mol Inform 2023; 42:e2200188. [PMID: 36262028 DOI: 10.1002/minf.202200188] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/19/2022] [Indexed: 11/11/2022]
Abstract
Structure-based virtual high-throughput screening involves docking chemical libraries to targets of interest. A parameter pertinent to the accuracy of the resulting pose is the root mean square deviation (RMSD) from a known crystallographic structure, i. e., the 'docking power'. Here, using a popular algorithm, Autodock Vina, as a model program, we evaluate the effects of varying two common docking parameters: the box size (the size of docking search space) and the exhaustiveness of the global search (the number of independent runs starting from random ligand conformations) on the RMSD from the PDBbind v2017 refined dataset of experimental protein-ligand complexes. Although it is clear that exhaustiveness is an important parameter, there is wide variation in the values used, with variation between 1 and >100. We, therefore, evaluated a combination of cubic boxes of different sizes and five exhaustiveness values (1, 8, 25, 50, 75, 100) within the range of those commonly adopted. The results show that the default exhaustiveness value of 8 performs well overall for most box sizes. In contrast, for all box sizes, but particularly for large boxes, an exhaustiveness value of 1 led to significantly higher median RMSD (mRMSD) values. The docking power was slightly improved with an exhaustiveness of 25, but the mRMSD changes little with values higher than 25. Therefore, although low exhaustiveness is computationally faster, the results are more likely to be far from reality, and, conversely, values >25 led to little improvement at the expense of computational resources. Overall, we recommend users to use at least the default exhaustiveness value of 8 for virtual screening calculations.
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Affiliation(s)
- Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6309, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 14311 Cumberland Avenue, Knoxville, TN 37996-1939, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37831-6309, USA.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, 14311 Cumberland Avenue, Knoxville, TN 37996-1939, USA
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20
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Shen Y, Parks JM, Smith JC. HLA Class I Supertype Classification Based on Structural Similarity. J Immunol 2023; 210:103-114. [PMID: 36453976 DOI: 10.4049/jimmunol.2200685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/31/2022] [Indexed: 12/24/2022]
Abstract
HLA class I proteins, a critical component in adaptive immunity, bind and present intracellular Ags to CD8+ T cells. The extreme polymorphism of HLA genes and associated peptide binding specificities leads to challenges in various endeavors, including neoantigen vaccine development, disease association studies, and HLA typing. Supertype classification, defined by clustering functionally similar HLA alleles, has proven helpful in reducing the complexity of distinguishing alleles. However, determining supertypes via experiments is impractical, and current in silico classification methods exhibit limitations in stability and functional relevance. In this study, by incorporating three-dimensional structures we present a method for classifying HLA class I molecules with improved breadth, accuracy, stability, and flexibility. Critical for these advances is our finding that structural similarity highly correlates with peptide binding specificity. The new classification should be broadly useful in peptide-based vaccine development and HLA-disease association studies.
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Affiliation(s)
- Yue Shen
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN; and
| | - Jeremy C Smith
- UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN.,Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN; and.,Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN
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21
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Tan L, Smith MD, Scott HL, Yahya A, Elkins JG, Katsaras J, O'Neill HM, Pingali SV, Smith JC, Davison BH, Nickels JD. Modeling the partitioning of amphiphilic molecules and co-solvents in biomembranes. J Appl Crystallogr 2022. [DOI: 10.1107/s1600576722008998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Amphiphilic co-solvents can have a significant impact on the structure, organization and physical properties of lipid bilayers. Describing the mutual impact of partitioning and induced structure changes is therefore a crucial consideration for a range of topics such as anesthesia and other pharmacokinetic effects, as well as microbial solvent tolerance in the production of biofuels and other fermentation products, where molecules such as ethanol, butanol or acetic acid might be generated. Small-angle neutron scattering (SANS) is a key method for studying lipid and polymer bilayer structures, with many models for extracting bilayer structure (thickness, area per lipid etc.) from scattering data in use today. However, the molecular details of co-solvent partitioning are conflated with induced changes to bilayer structure, making interpretation and modeling of the scattering curves a challenge with the existing set of models. To address this, a model of a bilayer structure is presented which invokes a two-term partition constant accounting for the localization of the co-solvent within the bilayer. This model was validated using a series of SANS measurements of lipid vesicles in the presence of the co-solvent tetrahydrofuran (THF), showing several strategies of how to deploy the two-parameter partition constant model to describe scattering data and extract both structure and partitioning information from the data. Molecular dynamics simulations are then used to evaluate assumptions of the model, provide additional molecular scale details and illustrate its complementary nature to the data fitting procedure. This approach results in estimates of the partition coefficient for THF in 1,2-dimyristoyl-sn-glycero-3-phosphocholine at 35°C, along with an estimate of the fraction of THF residing in the hydrophobic core of the membrane. The authors envision that this model will be applicable to a wide range of other bilayer/amphiphile interactions and provide the associated code needed to implement this model as a fitting algorithm for scattering data in the SasView suite.
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22
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T. RR, Smith JC. Structural patterns in class 1 major histocompatibility complex‐restricted nonamer peptide binding to T‐cell receptors. Proteins 2022; 90:1645-1654. [DOI: 10.1002/prot.26343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 03/12/2022] [Accepted: 03/27/2022] [Indexed: 11/09/2022]
Affiliation(s)
- Rajitha Rajeshwar T.
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology University of Tennessee Knoxville Tennessee USA
- UT/ORNL Center for Molecular Biophysics Oak Ridge National Laboratory Oak Ridge Tennessee USA
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23
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Liu SH, Xiao Z, Mishra SK, Mitchell JC, Smith JC, Quarles LD, Petridis L. Identification of Small-Molecule Inhibitors of Fibroblast Growth Factor 23 Signaling via In Silico Hot Spot Prediction and Molecular Docking to α-Klotho. J Chem Inf Model 2022; 62:3627-3637. [PMID: 35868851 PMCID: PMC10018682 DOI: 10.1021/acs.jcim.2c00633] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fibroblast growth factor 23 (FGF23) is a therapeutic target for treating hereditary and acquired hypophosphatemic disorders, such as X-linked hypophosphatemic (XLH) rickets and tumor-induced osteomalacia (TIO), respectively. FGF23-induced hypophosphatemia is mediated by signaling through a ternary complex formed by FGF23, the FGF receptor (FGFR), and α-Klotho. Currently, disorders of excess FGF23 are treated with an FGF23-blocking antibody, burosumab. Small-molecule drugs that disrupt protein/protein interactions necessary for the ternary complex formation offer an alternative to disrupting FGF23 signaling. In this study, the FGF23:α-Klotho interface was targeted to identify small-molecule protein/protein interaction inhibitors since it was computationally predicted to have a large fraction of hot spots and two druggable residues on α-Klotho. We further identified Tyr433 on the KL1 domain of α-Klotho as a promising hot spot and α-Klotho as an appropriate drug-binding target at this interface. Subsequently, we performed in silico docking of ∼5.5 million compounds from the ZINC database to the interface region of α-Klotho from the ternary crystal structure. Following docking, 24 and 20 compounds were in the final list based on the lowest binding free energies to α-Klotho and the largest number of contacts with Tyr433, respectively. Five compounds were assessed experimentally by their FGF23-mediated extracellular signal-regulated kinase (ERK) activities in vitro, and two of these reduced activities significantly. Both these compounds were predicted to have favorable binding affinities to α-Klotho but not have a large number of contacts with the hot spot Tyr433. ZINC12409120 was found experimentally to disrupt FGF23:α-Klotho interaction to reduce FGF23-mediated ERK activities by 70% and have a half maximal inhibitory concentration (IC50) of 5.0 ± 0.23 μM. Molecular dynamics (MD) simulations of the ZINC12409120:α-Klotho complex starting from in silico docking poses reveal that the ligand exhibits contacts with residues on the KL1 domain, the KL1-KL2 linker, and the KL2 domain of α-Klotho simultaneously, thereby possibly disrupting the regular function of α-Klotho and impeding FGF23:α-Klotho interaction. ZINC12409120 is a candidate for lead optimization.
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Affiliation(s)
- Shih-Hsien Liu
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee37996, United States
| | - Zhousheng Xiao
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee38163, United States
| | - Sambit K Mishra
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee37996, United States
| | - L Darryl Quarles
- Department of Medicine, College of Medicine, University of Tennessee Health Science Center, Memphis, Tennessee38163, United States
| | - Loukas Petridis
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee37831, United States.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee37996, United States
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24
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Bensing BA, Stubbs HE, Agarwal R, Yamakawa I, Luong K, Solakyildirim K, Yu H, Hadadianpour A, Castro MA, Fialkowski KP, Morrison KM, Wawrzak Z, Chen X, Lebrilla CB, Baudry J, Smith JC, Sullam PM, Iverson TM. Origins of glycan selectivity in streptococcal Siglec-like adhesins suggest mechanisms of receptor adaptation. Nat Commun 2022; 13:2753. [PMID: 35585145 PMCID: PMC9117288 DOI: 10.1038/s41467-022-30509-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Accepted: 04/26/2022] [Indexed: 11/22/2022] Open
Abstract
Bacterial binding to host receptors underlies both commensalism and pathogenesis. Many streptococci adhere to protein-attached carbohydrates expressed on cell surfaces using Siglec-like binding regions (SLBRs). The precise glycan repertoire recognized may dictate whether the organism is a strict commensal versus a pathogen. However, it is currently not clear what drives receptor selectivity. Here, we use five representative SLBRs and identify regions of the receptor binding site that are hypervariable in sequence and structure. We show that these regions control the identity of the preferred carbohydrate ligand using chimeragenesis and single amino acid substitutions. We further evaluate how the identity of the preferred ligand affects the interaction with glycoprotein receptors in human saliva and plasma samples. As point mutations can change the preferred human receptor, these studies suggest how streptococci may adapt to changes in the environmental glycan repertoire.
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Affiliation(s)
- Barbara A Bensing
- Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA
- the Northern California Institute for Research and Education, San Francisco, CA, 94121, USA
| | - Haley E Stubbs
- Graduate Program in Chemical and Physical Biology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Rupesh Agarwal
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Izumi Yamakawa
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- School of Nursing, Belmont University, Nashville, TN, 37212, USA
| | - Kelvin Luong
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kemal Solakyildirim
- Department of Chemistry, Erzincan Binali Yildirim University, Erzincan, 24100, Turkey
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Azadeh Hadadianpour
- Department of Microbiology, Pathology, and Immunology, Vanderbilt University, Nashville, TN, 37232, USA
| | - Manuel A Castro
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA
| | - Kevin P Fialkowski
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA
- College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - KeAndreya M Morrison
- Department of Pharmacology, School of Graduate Studies and Research, Meharry Medical College, Nashville, TN, 37208, USA
| | - Zdzislaw Wawrzak
- LS-CAT Synchrotron Research Center, Northwestern University, Argonne, IL, 60439, USA
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Jerome Baudry
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL, 35899, USA
| | - Jeremy C Smith
- University of Tennessee/Oak Ridge National Laboratory, Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Paul M Sullam
- Division of Infectious Diseases, Veterans Affairs Medical Center, Department of Medicine, University of California, San Francisco, CA, USA
- the Northern California Institute for Research and Education, San Francisco, CA, 94121, USA
| | - T M Iverson
- Department of Pharmacology, Vanderbilt University, Nashville, TN, 37232, USA.
- Department of Biochemistry, Vanderbilt University, Nashville, TN, 37232, USA.
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25
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Leus IV, Weeks JW, Bonifay V, Shen Y, Yang L, Cooper CJ, Nash D, Duerfeldt AS, Smith JC, Parks JM, Rybenkov VV, Zgurskaya HI. Property space mapping of Pseudomonas aeruginosa permeability to small molecules. Sci Rep 2022; 12:8220. [PMID: 35581346 PMCID: PMC9114115 DOI: 10.1038/s41598-022-12376-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Accepted: 05/10/2022] [Indexed: 02/03/2023] Open
Abstract
Two membrane cell envelopes act as selective permeability barriers in Gram-negative bacteria, protecting cells against antibiotics and other small molecules. Significant efforts are being directed toward understanding how small molecules permeate these barriers. In this study, we developed an approach to analyze the permeation of compounds into Gram-negative bacteria and applied it to Pseudomonas aeruginosa, an important human pathogen notorious for resistance to multiple antibiotics. The approach uses mass spectrometric measurements of accumulation of a library of structurally diverse compounds in four isogenic strains of P. aeruginosa with varied permeability barriers. We further developed a machine learning algorithm that generates a deterministic classification model with minimal synonymity between the descriptors. This model predicted good permeators into P. aeruginosa with an accuracy of 89% and precision above 58%. The good permeators are broadly distributed in the property space and can be mapped to six distinct regions representing diverse chemical scaffolds. We posit that this approach can be used for more detailed mapping of the property space and for rational design of compounds with high Gram-negative permeability.
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Affiliation(s)
- Inga V Leus
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Jon W Weeks
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Vincent Bonifay
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Liang Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Connor J Cooper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Dinesh Nash
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA
| | - Adam S Duerfeldt
- Department of Medicinal Chemistry, University of Minnesota, 717 Delaware St. SE, Minneapolis, MN, 55414, USA
| | - Jeremy C Smith
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN, 37996, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Valentin V Rybenkov
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, USA.
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26
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Glaser J, Sedova A, Galanie S, Kneller DW, Davidson RB, Maradzike E, Del Galdo S, Labbé A, Hsu DJ, Agarwal R, Bykov D, Tharrington A, Parks JM, Smith DMA, Daidone I, Coates L, Kovalevsky A, Smith JC. Hit Expansion of a Noncovalent SARS-CoV-2 Main Protease Inhibitor. ACS Pharmacol Transl Sci 2022; 5:255-265. [PMID: 35434531 PMCID: PMC9003389 DOI: 10.1021/acsptsci.2c00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Indexed: 11/29/2022]
Abstract
![]()
Inhibition of the SARS-CoV-2 main
protease (Mpro) is
a major focus of drug discovery efforts against COVID-19. Here we
report a hit expansion of non-covalent inhibitors of Mpro. Starting from a recently discovered scaffold (The COVID Moonshot
Consortium. Open Science Discovery of Oral Non-Covalent SARS-CoV-2
Main Protease Inhibitor Therapeutics. bioRxiv 2020.10.29.339317) represented by an isoquinoline
series, we searched a database of over a billion compounds using a
cheminformatics molecular fingerprinting approach. We identified and
tested 48 compounds in enzyme inhibition assays, of which 21 exhibited
inhibitory activity above 50% at 20 μM. Among these,
four compounds with IC50 values around 1 μM
were found. Interestingly, despite the large search space, the isoquinolone
motif was conserved in each of these four strongest binders. Room-temperature
X-ray structures of co-crystallized protein–inhibitor complexes
were determined up to 1.9 Å resolution for two of these
compounds as well as one of the stronger inhibitors in the original
isoquinoline series, revealing essential interactions with the binding
site and water molecules. Molecular dynamics simulations and quantum
chemical calculations further elucidate the binding interactions as
well as electrostatic effects on ligand binding. The results help
explain the strength of this new non-covalent scaffold for Mpro inhibition and inform lead optimization efforts for this series,
while demonstrating the effectiveness of a high-throughput computational
approach to expanding a pharmacophore library.
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Affiliation(s)
- Jens Glaser
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Ada Sedova
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Stephanie Galanie
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,Protein Engineering, Merck, 126 East Lincoln Avenue, RY800-C303, Rahway, New Jersey 07065, United States
| | - Daniel W Kneller
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States.,New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Russell B Davidson
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Elvis Maradzike
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Sara Del Galdo
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Audrey Labbé
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Darren J Hsu
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Rupesh Agarwal
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dmytro Bykov
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Arnold Tharrington
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jerry M Parks
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Dayle M A Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, I-67010 L'Aquila, Italy
| | - Leighton Coates
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Andrey Kovalevsky
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
| | - Jeremy C Smith
- Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37830, United States
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27
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Perez I, Berndt S, Agarwal R, Castro MA, Vishnivetskiy SA, Smith JC, Sanders CR, Gurevich VV, Iverson T. A Model for the Signal Initiation Complex Between Arrestin-3 and the Src Family Kinase Fgr. J Mol Biol 2022; 434:167400. [PMID: 34902430 PMCID: PMC8752512 DOI: 10.1016/j.jmb.2021.167400] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Revised: 11/24/2021] [Accepted: 12/04/2021] [Indexed: 02/01/2023]
Abstract
Arrestins regulate a wide range of signaling events, most notably when bound to active G protein-coupled receptors (GPCRs). Among the known effectors recruited by GPCR-bound arrestins are Src family kinases, which regulate cellular growth and proliferation. Here, we focus on arrestin-3 interactions with Fgr kinase, a member of the Src family. Previous reports demonstrated that Fgr exhibits high constitutive activity, but can be further activated by both arrestin-dependent and arrestin-independent pathways. We report that arrestin-3 modulates Fgr activity with a hallmark bell-shaped concentration-dependence, consistent with a role as a signaling scaffold. We further demonstrate using NMR spectroscopy that a polyproline motif within arrestin-3 interacts directly with the SH3 domain of Fgr. To provide a framework for this interaction, we determined the crystal structure of the Fgr SH3 domain at 1.9 Å resolution and developed a model for the GPCR-arrestin-3-Fgr complex that is supported by mutagenesis. This model suggests that Fgr interacts with arrestin-3 at multiple sites and is consistent with the locations of disease-associated Fgr mutations. Collectively, these studies provide a structural framework for arrestin-dependent activation of Fgr.
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Affiliation(s)
- Ivette Perez
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146;,Center for Structural Biology, Nashville, TN 37232-0146
| | - Sandra Berndt
- Department of Pharmacology, Vanderbilt University, Nashville, TN 37232-0146;,Center for Structural Biology, Nashville, TN 37232-0146
| | - Rupesh Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996;,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN
| | - Manuel A. Castro
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146;,Center for Structural Biology, Nashville, TN 37232-0146
| | | | - Jeremy C. Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996;,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, TN
| | - Charles R. Sanders
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146;,Center for Structural Biology, Nashville, TN 37232-0146
| | | | - T.M. Iverson
- Department of Biochemistry, Vanderbilt University, Nashville, TN 37232-0146;,Department of Pharmacology, Vanderbilt University, Nashville, TN 37232-0146;,Center for Structural Biology, Nashville, TN 37232-0146;,Vanderbilt Institute of Chemical Biology, Nashville, TN 37232-0146
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28
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dhiman I, C. Berg M, Petridis L, Smith JC, Gautam S. Dynamic odd-even effect in n-alkane systems: A molecular dynamics study. Phys Chem Chem Phys 2022; 24:28403-28410. [DOI: 10.1039/d2cp02760g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Alternation in various properties of n-alkanes (CnH2n+2) as a function of carbon content (n) is termed `odd-even effect'. Here, we report a comprehensive molecular dynamics simulation study on n-alkane systems...
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29
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Mamontov E, Bordallo HN, Delaire O, Nickels J, Peters J, Schneider GJ, Smith JC, Sokolov AP. Broadband Wide-Angle VElocity Selector (BWAVES) neutron spectrometer designed for the SNS Second Target Station. EPJ Web Conf 2022. [DOI: 10.1051/epjconf/202227202003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A recently proposed wide-angle velocity selector (WAVES) device for choosing the velocity of detected neutrons after they have been scattered by the sample paves the way for inverted geometry neutron spectrometers with continuously adjustable final neutron wavelength. BWAVES broadband inverted geometry spectrometer proposed for the Second Target Station at the Spallation Neutron Source at Oak Ridge National Laboratory is designed using WAVES to simultaneously probe dynamic processes spanning 4.5 decades in time (energy transfer). This makes BWAVES a uniquely flexible instrument which can be viewed as either a quasielasitc neutron scattering (QENS) spectrometer with a practically unlimited (overlapping with the vibrational excitations) range of energy transfers, or a broadband inelastic vibrational neutron spectrometer with QENS capabilities, including a range of accessible momentum transfer (Q) and a sufficiently high energy resolution at the elastic line. The new capabilities offered by BWAVES will expand the application of neutron scattering in ways not possible with existing neutron spectrometers.
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30
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Li J, Xie J, Godec A, Weninger KR, Liu C, Smith JC, Hong L. Non-ergodicity of a globular protein extending beyond its functional timescale. Chem Sci 2022; 13:9668-9677. [PMID: 36091909 PMCID: PMC9400594 DOI: 10.1039/d2sc03069a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble. Here, by performing single-molecule fluorescence resonance energy transfer (smFRET) experiments and molecular dynamics (MD) simulations of a multi-domain globular protein, cytoplasmic protein-tyrosine phosphatase (SHP2), we demonstrate that the functional inter-domain motion is observationally non-ergodic over the time spans 10−12 to 10−7 s and 10−1 to 102 s. The difference between observational non-ergodicity and simple non-convergence is discussed. In comparison, a single-strand DNA of similar size behaves ergodically with an energy landscape resembling a one-dimensional linear chain. The observed non-ergodicity results from the hierarchical connectivity of the high-dimensional energy landscape of the protein molecule. As the characteristic time for the protein to conduct its dephosphorylation function is ∼10 s, our findings suggest that, due to the non-ergodicity, individual, seemingly identical protein molecules can be dynamically and functionally different. Internal motions of folded proteins have been assumed to be ergodic, i.e., that the dynamics of a single protein molecule averaged over a very long time resembles that of an ensemble.![]()
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Affiliation(s)
- Jun Li
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
| | - JingFei Xie
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
- University of the Chinese Academy of Sciences, Beijing 100049, China
| | - Aljaž Godec
- Mathematical BioPhysics Group, Max Planck Institute for Biophysical Chemistry, Göttingen 37077, Germany
| | - Keith R. Weninger
- Department of Physics, North Carolina State University, Raleigh, NC 27695, USA
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Center for Excellence in Molecular Synthesis, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201203, China
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Liang Hong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai 200240, China
- Institute of Natural Sciences, Shanghai Jiao Tong University, Shanghai 200240, China
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31
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Gumbart JC, Ferreira JL, Hwang H, Hazel AJ, Cooper CJ, Parks JM, Smith JC, Zgurskaya HI, Beeby M. Lpp positions peptidoglycan at the AcrA-TolC interface in the AcrAB-TolC multidrug efflux pump. Biophys J 2021; 120:3973-3982. [PMID: 34411576 DOI: 10.1016/j.bpj.2021.08.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 07/02/2021] [Accepted: 08/11/2021] [Indexed: 01/07/2023] Open
Abstract
The multidrug efflux pumps of Gram-negative bacteria are a class of complexes that span the periplasm, coupling both the inner and outer membranes to expel toxic molecules. The best-characterized example of these tripartite pumps is the AcrAB-TolC complex of Escherichia coli. However, how the complex interacts with the peptidoglycan (PG) cell wall, which is anchored to the outer membrane (OM) by Braun's lipoprotein (Lpp), is still largely unknown. In this work, we present molecular dynamics simulations of a complete, atomistic model of the AcrAB-TolC complex with the inner membrane, OM, and PG layers all present. We find that the PG localizes to the junction of AcrA and TolC, in agreement with recent cryo-tomography data. Free-energy calculations reveal that the positioning of PG is determined by the length and conformation of multiple Lpp copies anchoring it to the OM. The distance between the PG and OM measured in cryo-electron microscopy images of wild-type E. coli also agrees with the simulation-derived spacing. Sequence analysis of AcrA suggests a conserved role for interactions with PG in the assembly and stabilization of efflux pumps, one that may extend to other trans-envelope complexes as well.
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Affiliation(s)
- James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia.
| | - Josie L Ferreira
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Hyea Hwang
- School of Materials Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia
| | - Anthony J Hazel
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia
| | - Connor J Cooper
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee; Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Helen I Zgurskaya
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
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Smith JC. Locking out water at 100°C. Biophys J 2021; 120:3541. [PMID: 34358450 PMCID: PMC8456173 DOI: 10.1016/j.bpj.2021.07.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/25/2021] [Accepted: 07/19/2021] [Indexed: 11/28/2022] Open
Affiliation(s)
- Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee.
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T RR, Saharay M, Smith JC, Krishnan M. Correlated Response of Protein Side-Chain Fluctuations and Conformational Entropy to Ligand Binding. J Phys Chem B 2021; 125:9641-9651. [PMID: 34423989 DOI: 10.1021/acs.jpcb.1c01227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The heterogeneous fast side-chain dynamics of proteins plays crucial roles in molecular recognition and binding. Site-specific NMR experiments quantify these motions by measuring the model-free order parameter (Oaxis2) on a scale of 0 (most flexible) to 1 (least flexible) for each methyl-containing residue of proteins. Here, we have examined ligand-induced variations in the fast side-chain dynamics and conformational entropy of calmodulin (CaM) using five different CaM-peptide complexes. Oaxis2 of CaM in the ligand-free (Oaxis,U2) and ligand-bound (Oaxis,B2) states are calculated from molecular dynamics trajectories and conformational energy surfaces obtained using the adaptive biasing force (ABF) method. ΔOaxis2 = Oaxis,B2 - Oaxis,U2 follows a Gaussian-like unimodal distribution whose second moment is a potential indicator of the binding affinity of these complexes. The probability for the binding-induced Oaxis,U2 → Oaxis,B2 transition decreases with increasing magnitude of ΔOaxis2, indicating that large flexibility changes are improbable for side chains of CaM after ligand binding. A linear correlation established between ΔOaxis2 and the conformational entropy change of the protein makes possible the determination of the conformational entropy of binding of protein-ligand complexes. The results not only underscore the functional importance of fast side-chain fluctuations but also highlight key motional and thermodynamic correlates of protein-ligand binding.
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Affiliation(s)
- Rajitha Rajeshwar T
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States.,UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, P.O. Box 2008, Oak Ridge, Tennessee 37831-6309, United States
| | - Marimuthu Krishnan
- Center for Computational Natural Sciences and Bioinformatics (CCNSB), International Institute of Information Technology, Gachibowli, Hyderabad 500032, India
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34
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Aranha MP, Penfound TA, Salehi S, Botteaux A, Smeesters P, Dale JB, Smith JC. Design of Broadly Cross-Reactive M Protein-Based Group A Streptococcal Vaccines. J Immunol 2021; 207:1138-1149. [PMID: 34341168 DOI: 10.4049/jimmunol.2100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 06/13/2021] [Indexed: 11/19/2022]
Abstract
Group A streptococcal infections are a significant cause of global morbidity and mortality. A leading vaccine candidate is the surface M protein, a major virulence determinant and protective Ag. One obstacle to the development of M protein-based vaccines is the >200 different M types defined by the N-terminal sequences that contain protective epitopes. Despite sequence variability, M proteins share coiled-coil structural motifs that bind host proteins required for virulence. In this study, we exploit this potential Achilles heel of conserved structure to predict cross-reactive M peptides that could serve as broadly protective vaccine Ags. Combining sequences with structural predictions, six heterologous M peptides in a sequence-related cluster were predicted to elicit cross-reactive Abs with the remaining five nonvaccine M types in the cluster. The six-valent vaccine elicited Abs in rabbits that reacted with all 11 M peptides in the cluster and functional opsonic Abs against vaccine and nonvaccine M types in the cluster. We next immunized mice with four sequence-unrelated M peptides predicted to contain different coiled-coil propensities and tested the antisera for cross-reactivity against 41 heterologous M peptides. Based on these results, we developed an improved algorithm to select cross-reactive peptide pairs using additional parameters of coiled-coil length and propensity. The revised algorithm accurately predicted cross-reactive Ab binding, improving the Matthews correlation coefficient from 0.42 to 0.74. These results form the basis for selecting the minimum number of N-terminal M peptides to include in potentially broadly efficacious multivalent vaccines that could impact the overall global burden of group A streptococcal diseases.
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Affiliation(s)
- Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN; .,Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
| | - Thomas A Penfound
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN
| | - Sanaz Salehi
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN
| | - Anne Botteaux
- Molecular Bacteriology Laboratory, Free University of Brussels, Brussels, Belgium
| | - Pierre Smeesters
- Molecular Bacteriology Laboratory, Free University of Brussels, Brussels, Belgium.,Academic Children's Hospital Queen Fabiola, Free University of Brussels, Brussels, Belgium; and.,Centre for International Child Health, University of Melbourne, Melbourne, Victoria, Australia
| | - James B Dale
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN;
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN; .,Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN
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35
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Lotufo GR, Boyd RE, Harmon AR, Bednar AJ, Smith JC, Simini M, Sunahara GI, Hawari J, Kuperman RG. Accumulation of Insensitive Munition Compounds in the Earthworm Eisenia andrei from Amended Soil: Methodological Considerations for Determination of Bioaccumulation Factors. Environ Toxicol Chem 2021; 40:1713-1725. [PMID: 33646621 DOI: 10.1002/etc.5028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/11/2021] [Accepted: 02/26/2021] [Indexed: 06/12/2023]
Abstract
The present study investigates the bioaccumulation of the insensitive munition compounds 2,4-dinitroanisole (DNAN) and 3-nitro-1,2,4-triazol-5-one (NTO), developed for future weapons systems to replace current munitions containing sensitive explosives. The earthworm Eisenia andrei was exposed to sublethal concentrations of DNAN or NTO amended in Sassafras sandy loam. Chemical analysis indicated that 2- and 4-amino-nitroanisole (2-ANAN and 4-ANAN, respectively) were formed in DNAN-amended soils. The SumDNAN (sum of DNAN, 2-ANAN, and 4-ANAN concentrations) in soil decreased by 40% during the 14-d exposure period. The SumDNAN in the earthworm body residue increased until day 3 and decreased thereafter. Between days 3 and 14, there was a 73% decrease in tissue uptake that was greater than the 23% decrease in the soil concentration, suggesting that the bioavailable fraction may have decreased over time. By day 14, the DNAN concentration accounted for only 45% of the SumDNAN soil concentration, indicating substantial DNAN transformation in the presence of earthworms. The highest bioaccumulation factor (BAF; the tissue-to-soil concentration ratio) was 6.2 ± 1.0 kg/kg (dry wt) on day 3 and decreased to 3.8 ± 0.8 kg/kg by day 14. Kinetic studies indicated a BAF of 2.3 kg/kg, based on the earthworm DNAN uptake rate of 2.0 ± 0.24 kg/kg/d, compared with the SumDNAN elimination rate of 0.87 d-1 (half-life = 0.79 d). The compound DNAN has a similar potential to bioaccumulate from soil compared with trinitrotoluene. The NTO concentration in amended soil decreased by 57% from the initial concentration (837 mg NTO/kg dry soil) during 14 d, likely due to the formation of unknown transformation products. The bioaccumulation of NTO was negligible (BAF ≤ 0.018 kg/kg dry wt). Environ Toxicol Chem 2021;40:1713-1725. © 2021 SETAC. This article has been contributed to by US Government employees and their work is in the public domain in the USA.
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Affiliation(s)
- G R Lotufo
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, Mississippi, USA
| | - R E Boyd
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, Mississippi, USA
| | - A R Harmon
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, Mississippi, USA
| | - A J Bednar
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, Mississippi, USA
| | - J C Smith
- Environmental Laboratory, Engineer Research and Development Center, US Army, Vicksburg, Mississippi, USA
| | - M Simini
- US Army Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
| | - G I Sunahara
- Department of Natural Resource Sciences, McGill University, Ste-Anne-de-Bellevue, QC, Canada
| | - J Hawari
- Department of Civil, Geological and Mining Engineering, Polytechnique Montreal, Montreal, QC, Canada
| | - R G Kuperman
- US Army Chemical Biological Center, Aberdeen Proving Ground, Maryland, USA
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36
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Xiao Z, Liu J, Liu SH, Petridis L, Cai C, Cao L, Wang G, Chin AL, Cleveland JW, Ikedionwu MO, Carrick JD, Smith JC, Quarles LD. Novel Small Molecule Fibroblast Growth Factor 23 Inhibitors Increase Serum Phosphate and Improve Skeletal Abnormalities in Hyp Mice. Mol Pharmacol 2021; 101:408-421. [PMID: 35339985 PMCID: PMC11033927 DOI: 10.1124/molpharm.121.000471] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/20/2022] [Indexed: 11/22/2022] Open
Abstract
Excess fibroblast growth factor (FGF) 23 causes hereditary hypophosphatemic rickets, such as X-linked hypophosphatemia (XLH) and tumor-induced osteomalacia (TIO). A small molecule that specifically binds to FGF23 to prevent activation of the fibroblast growth factor receptor/α-Klotho complex has potential advantages over the currently approved systemically administered FGF23 blocking antibody. Using structure-based drug design, we previously identified ZINC13407541 (N-[[2-(2-phenylethenyl)cyclopenten-1-yl]methylidene]hydroxylamine) as a small molecule antagonist for FGF23. Additional structure-activity studies developed a series of ZINC13407541 analogs with enhanced drug-like properties. In this study, we tested in a preclinical Hyp mouse homolog of XLH a direct connect analog [(E)-2-(4-(tert-butyl)phenyl)cyclopent-1-ene-1-carbaldehyde oxime] (8n), which exhibited the greatest stability in microsomal assays, and [(E)-2-((E)-4-methylstyryl)benzaldehyde oxime] (13a), which exhibited increased in vitro potency. Using cryo-electron microscopy structure and computational docking, we identified a key binding residue (Q156) of the FGF23 antagonists, ZINC13407541, and its analogs (8n and 13a) in the N-terminal domain of FGF23 protein. Site-directed mutagenesis and bimolecular fluorescence complementation-fluorescence resonance energy transfer assay confirmed the binding site of these three antagonists. We found that pharmacological inhibition of FGF23 with either of these compounds blocked FGF23 signaling and increased serum phosphate and 1,25-dihydroxyvitamin D [1,25(OH)2D] concentrations in Hyp mice. Long-term parenteral treatment with 8n or 13a also enhanced linear bone growth, increased mineralization of bone, and narrowed the growth plate in Hyp mice. The more potent 13a compound had greater therapeutic effects in Hyp mice. Further optimization of these FGF23 inhibitors may lead to versatile drugs to treat excess FGF23-mediated disorders. SIGNIFICANCE STATEMENT: This study used structure-based drug design and medicinal chemistry approaches to identify and optimize small molecules with different stability and potency, which antagonize excessive actions of fibroblast growth factor 23 (FGF23) in hereditary hypophosphatemic rickets. The findings confirmed that these antagonists bind to the N-terminus of FGF23 to inhibit its binding to and activation of the fibroblast growth factor receptors/α-Klotho signaling complex. Administration of these lead compounds improved phosphate homeostasis and abnormal skeletal phenotypes in a preclinical Hyp mouse model.
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Affiliation(s)
- Zhousheng Xiao
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Jiawang Liu
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Shih-Hsien Liu
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Loukas Petridis
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Chun Cai
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Li Cao
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Guangwei Wang
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Ai Lin Chin
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Jacob W Cleveland
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Munachi O Ikedionwu
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Jesse D Carrick
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Jeremy C Smith
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
| | - Leigh Darryl Quarles
- Department of Medicine, College of Medicine (Z.X., C.C., L.C., G.W.W., L.D.Q.) and Department of Pharmaceutical Sciences, College of Pharmacy (J.L.), University of Tennessee Health Science Center, Memphis, Tennessee; University of Tennessee (UT)/Oak Ridge National Laboratory (ORNL) Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, Tennessee (S.H.L., L.P., J.C.S.); Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee (L.P., J.C.S.); and Department of Chemistry, Tennessee Technological University, Cookeville, Tennessee (A.L.C., J.W.C., M.O.I., J.D.C.)
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37
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design. J Phys Chem Lett 2021; 12:4195-4202. [PMID: 33900080 PMCID: PMC8097931 DOI: 10.1021/acs.jpclett.1c00425] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 04/21/2021] [Indexed: 05/03/2023]
Abstract
The catalytic reaction in SARS-CoV-2 main protease is activated by a proton transfer (PT) from Cys145 to His41. The same PT is likely also required for the covalent binding of some inhibitors. Here we use a multiscale computational approach to investigate the PT thermodynamics in the apo enzyme and in complex with two potent inhibitors, N3 and the α-ketoamide 13b. We show that with the inhibitors the free energy cost to reach the charge-separated state of the active-site dyad is lower, with N3 inducing the most significant reduction. We also show that a few key sites (including specific water molecules) significantly enhance or reduce the thermodynamic feasibility of the PT reaction, with selective desolvation of the active site playing a crucial role. The approach presented is a cost-effective procedure to identify the enzyme regions that control the activation of the catalytic reaction and is thus also useful to guide the design of inhibitors.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center
S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
| | - Chris Chipot
- UMR 7019, Université de Lorraine, Laboratoire
International Associé CNRS, 54506 Vandœuvre-lès-Nancy, France
- University
of Illinois at Urbana−Champaign, 1110 West Green Street, Urbana, Illinois 61801, United States
| | - James C. Gumbart
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Diane L. Lynch
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Anna Pavlova
- School
of Physics, Georgia Institute of Technology, Atlanta Georgia 30332, United States
| | - Jeremy C. Smith
- Department
of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville, 309 Ken and Blaire Mossman Bldg., 1311 Cumberland
Avenue, Knoxville, Tennessee 37996, United States
- UT/ORNL
Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Isabella Daidone
- Department
of Physical and Chemical Sciences, University
of L’Aquila, Via
Vetoio, I-67010 L’Aquila, Italy
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38
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Collart C, Ciccarelli A, Ivanovitch K, Rosewell I, Kumar S, Kelly G, Edwards A, Smith JC. The migratory pathways of the cells that form the endocardium, dorsal aortae, and head vasculature in the mouse embryo. BMC Dev Biol 2021; 21:8. [PMID: 33752600 PMCID: PMC7986287 DOI: 10.1186/s12861-021-00239-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 02/12/2021] [Indexed: 11/25/2022]
Abstract
Background Vasculogenesis in amniotes is often viewed as two spatially and temporally distinct processes, occurring in the yolk sac and in the embryo. However, the spatial origins of the cells that form the primary intra-embryonic vasculature remain uncertain. In particular, do they obtain their haemato-endothelial cell fate in situ, or do they migrate from elsewhere? Recently developed imaging techniques, together with new Tal1 and existing Flk1 reporter mouse lines, have allowed us to investigate this question directly, by visualising cell trajectories live and in three dimensions. Results We describe the pathways that cells follow to form the primary embryonic circulatory system in the mouse embryo. In particular, we show that Tal1-positive cells migrate from within the yolk sac, at its distal border, to contribute to the endocardium, dorsal aortae and head vasculature. Other Tal1 positive cells, similarly activated within the yolk sac, contribute to the yolk sac vasculature. Using single-cell transcriptomics and our imaging, we identify VEGF and Apela as potential chemo-attractants that may regulate the migration into the embryo. The dorsal aortae and head vasculature are known sites of secondary haematopoiesis; given the common origins that we observe, we investigate whether this is also the case for the endocardium. We discover cells budding from the wall of the endocardium with high Tal1 expression and diminished Flk1 expression, indicative of an endothelial to haematopoietic transition. Conclusions In contrast to the view that the yolk sac and embryonic circulatory systems form by two separate processes, our results indicate that Tal1-positive cells from the yolk sac contribute to both vascular systems. It may be that initial Tal1 activation in these cells is through a common mechanism. Supplementary Information The online version contains supplementary material available at 10.1186/s12861-021-00239-3.
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Affiliation(s)
- C Collart
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
| | - A Ciccarelli
- Advanced Light Microscopy Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - K Ivanovitch
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - I Rosewell
- Genetic Modification Service, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - S Kumar
- Advanced Light Microscopy Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.,Photonics Group, 606 Blackett Laboratory, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - G Kelly
- Bioinformatics and Biostatistics Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - A Edwards
- Advanced Sequencing Facility, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - J C Smith
- Developmental Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
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Spencer JA, Penfound T, Salehi S, Aranha MP, Wade LE, Agarwal R, Smith JC, Dale JB, Baudry J. Cross-reactive immunogenicity of group A streptococcal vaccines designed using a recurrent neural network to identify conserved M protein linear epitopes. Vaccine 2021; 39:1773-1779. [PMID: 33642159 DOI: 10.1016/j.vaccine.2021.01.075] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/27/2021] [Accepted: 01/30/2021] [Indexed: 12/27/2022]
Abstract
The M protein of group A streptococci (Strep A) is a major virulence determinant and protective antigen. The N-terminal sequence of the protein defines the more than 200 M types of Strep A and also contains epitopes that elicit opsonic antibodies, some of which cross-react with heterologous M types. Current efforts to develop broadly protective M protein-based vaccines are directed at identifying potential cross-protective epitopes located in the N-terminal regions of cluster-related M proteins for use as vaccine antigens. In this study, we have used a comprehensive approach using the recurrent neural network ABCpred and IEDB epitope conservancy analysis tools to predict 16 residue linear B-cell epitopes from 117 clinically relevant M types of Strep A (~88% of global Strep A infections). To examine the immunogenicity of these epitope-based vaccines, nine peptides that together shared ≥60% sequence identity with 37 heterologous M proteins were incorporated into two recombinant hybrid protein vaccines, in which the epitopes were repeated 2 or 3 times, respectively. The combined immune responses of immunized rabbits showed that the vaccines elicited significant levels of antibodies against all nine vaccine epitopes present in homologous N-terminal 1-50 amino acid synthetic M peptides, as well as cross-reactive antibodies against 16 of 37 heterologous M peptides predicted to contain similar epitopes. The epitope-specificity of the cross-reactive antibodies was confirmed by ELISA inhibition assays and functional opsonic activity was assayed in HL-60-based bactericidal assays. The results provide important information for the future design of broadly protective M protein-based Strep A vaccines.
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Affiliation(s)
- Jay A Spencer
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, United States
| | - Tom Penfound
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Sanaz Salehi
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Lauren E Wade
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Rupesh Agarwal
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - James B Dale
- Department of Medicine, Division of Infectious Diseases, University of Tennessee Health Science Center, Memphis, TN 38163, United States
| | - Jerome Baudry
- Department of Biological Sciences, The University of Alabama in Huntsville, Huntsville, AL 35899, United States.
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40
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Topham CM, Smith JC. Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases. J Comput Aided Mol Des 2021; 35:355-369. [PMID: 33624202 DOI: 10.1007/s10822-021-00375-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/03/2021] [Indexed: 10/22/2022]
Abstract
Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.
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Affiliation(s)
- Christopher M Topham
- Molecular Forces Consulting, 24 Avenue Jacques Besse, 81500, Lavaur, France.
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany.
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA.
| | - Jeremy C Smith
- Computational Molecular Biophysics, IWR Der Universität Heidelberg, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
- Center for Molecular Biophysics, University of Tennessee / Oak Ridge National Laboratory, P.O.Box 2008, Oak Ridge, TN, 37831-6309, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, TN, 37996, USA
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41
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Shrestha UR, Smith JC, Petridis L. Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations. Commun Biol 2021; 4:243. [PMID: 33623120 PMCID: PMC7902620 DOI: 10.1038/s42003-021-01759-1] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from limitations of inaccuracy. Here, we show that enhancing the sampling using Hamiltonian replica-exchange MD (HREMD) led to unbiased and accurate ensembles, reproducing small-angle scattering and NMR chemical shift experiments, for three IDPs of varying sequence properties using two recently optimized force fields, indicating the general applicability of HREMD for IDPs. We further demonstrate that, unlike HREMD, standard MD can reproduce experimental NMR chemical shifts, but not small-angle scattering data, suggesting chemical shifts are insufficient for testing the validity of IDP ensembles. Surprisingly, we reveal that despite differences in their sequence, the inter-chain statistics of all three IDPs are similar for short contour lengths (< 10 residues). The results suggest that the major hurdle of generating an accurate unbiased ensemble for IDPs has now been largely overcome.
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Affiliation(s)
- Utsab R Shrestha
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
| | - Jeremy C Smith
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA
| | - Loukas Petridis
- Oak Ridge National Laboratory, Biosciences Division, UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, USA.
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, USA.
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42
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Ajina R, Malchiodi ZX, Fitzgerald AA, Zuo A, Wang S, Moussa M, Cooper CJ, Shen Y, Johnson QR, Parks JM, Smith JC, Catalfamo M, Fertig EJ, Jablonski SA, Weiner LM. Antitumor T-cell Immunity Contributes to Pancreatic Cancer Immune Resistance. Cancer Immunol Res 2021; 9:386-400. [PMID: 33509790 DOI: 10.1158/2326-6066.cir-20-0272] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 10/27/2020] [Accepted: 01/26/2021] [Indexed: 12/14/2022]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is the third leading cause of cancer death in the United States. Pancreatic tumors are minimally infiltrated by T cells and are largely refractory to immunotherapy. Accordingly, the role of T-cell immunity in pancreatic cancer has been somewhat overlooked. Here, we hypothesized that immune resistance in pancreatic cancer was induced in response to antitumor T-cell immune responses and that understanding how pancreatic tumors respond to immune attack may facilitate the development of more effective therapeutic strategies. We now provide evidence that T-cell-dependent host immune responses induce a PDAC-derived myeloid mimicry phenomenon and stimulate immune resistance. Three KPC mouse models of pancreatic cancer were used: the mT3-2D (Kras+/LSL-G12D; Trp53+/LSL-R172H; Pdx1-Cre) subcutaneous and orthotopic models, as well as the KP1 (p48-CRE/LSL-Kras/Trp53 flox/flox ) subcutaneous model. KPC cancer cells were grown in immunocompetent and immunodeficient C57BL/6 mice and analyzed to determine the impact of adaptive immunity on malignant epithelial cells, as well as on whole tumors. We found that induced T-cell antitumor immunity, via signal transducer and activator of transcription 1 (STAT1), stimulated malignant epithelial pancreatic cells to induce the expression of genes typically expressed by myeloid cells and altered intratumoral immunosuppressive myeloid cell profiles. Targeting the Janus Kinase (JAK)/STAT signaling pathway using the FDA-approved drug ruxolitinib overcame these tumor-protective responses and improved anti-PD-1 therapeutic efficacy. These findings provide future directions for treatments that specifically disable this mechanism of resistance in PDAC.
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Affiliation(s)
- Reham Ajina
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Zoe X Malchiodi
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Allison A Fitzgerald
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Annie Zuo
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Shangzi Wang
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Maha Moussa
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Connor J Cooper
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Yue Shen
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee
| | - Quentin R Johnson
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia
| | - Jerry M Parks
- Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, Tennessee.,Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia
| | - Jeremy C Smith
- Department of Chemistry and Biochemistry, Berry College, Mount Berry, Georgia.,Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee
| | - Marta Catalfamo
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, District of Columbia
| | - Elana J Fertig
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Applied Mathematics and Statistics, Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland.,Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sandra A Jablonski
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia
| | - Louis M Weiner
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, District of Columbia.
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43
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Pavlova A, Lynch DL, Daidone I, Zanetti-Polzi L, Smith MD, Chipot C, Kneller DW, Kovalevsky A, Coates L, Golosov AA, Dickson CJ, Velez-Vega C, Duca JS, Vermaas JV, Pang YT, Acharya A, Parks JM, Smith JC, Gumbart JC. Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease. Chem Sci 2021; 12:1513-1527. [PMID: 35356437 PMCID: PMC8899719 DOI: 10.1039/d0sc04942e] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022] Open
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41–Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nucleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an α-ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored Nδ (HD) and Nϵ (HE) protonation of His41 and His164, respectively, the α-ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts. The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics.![]()
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Vermaas JV, Sedova A, Baker MB, Boehm S, Rogers DM, Larkin J, Glaser J, Smith MD, Hernandez O, Smith JC. Supercomputing Pipelines Search for Therapeutics Against COVID-19. Comput Sci Eng 2021; 23:7-16. [PMID: 35939280 PMCID: PMC9280802 DOI: 10.1109/mcse.2020.3036540] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/31/2020] [Accepted: 11/03/2020] [Indexed: 11/15/2022]
Abstract
The urgent search for drugs to combat SARS-CoV-2 has included the use of supercomputers. The use of general-purpose graphical processing units (GPUs), massive parallelism, and new software for high-performance computing (HPC) has allowed researchers to search the vast chemical space of potential drugs faster than ever before. We developed a new drug discovery pipeline using the Summit supercomputer at Oak Ridge National Laboratory to help pioneer this effort, with new platforms that incorporate GPU-accelerated simulation and allow for the virtual screening of billions of potential drug compounds in days compared to weeks or months for their ability to inhibit SARS-COV-2 proteins. This effort will accelerate the process of developing drugs to combat the current COVID-19 pandemic and other diseases.
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Affiliation(s)
| | - Ada Sedova
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Swen Boehm
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Jens Glaser
- Oak Ridge National Laboratory, Oak Ridge, TN, USA
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45
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Zanetti-Polzi L, Smith MD, Chipot C, Gumbart JC, Lynch DL, Pavlova A, Smith JC, Daidone I. Tuning Proton Transfer Thermodynamics in SARS-Cov-2 Main Protease: Implications for Catalysis and Inhibitor Design. ChemRxiv 2020:13200227. [PMID: 33200115 PMCID: PMC7668740 DOI: 10.26434/chemrxiv.13200227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Revised: 11/06/2020] [Indexed: 12/21/2022]
Abstract
In this comutational work a hybrid quantum mechanics/molecular mechanics approach, the MD-PMM approach, is used to investigate the proton transfer reaction the activates the catalytic activity of SARS-CoV-2 main protease. The proton transfer thermodynamics is investigated for the apo ensyme (i.e., without any bound substrate or inhibitor) and in the presence of a inhibitor, N3, which was previously shown to covalently bind SARS-CoV-2 main protease.
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Affiliation(s)
- Laura Zanetti-Polzi
- Center S3, CNR Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Micholas Dean Smith
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Chris Chipot
- UMR 7019, Universite de Lorraine, Laboratoire International Associe CNRS
- University of Illinois at Urbana-Champaign, 1110 West Green Street, Urbana, IL, 61801, United States
| | - James C Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Diane L Lynch
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Anna Pavlova
- School of Physics, Georgia Institute of Technology, Atlanta GA 30332, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, TN 37831, United States
- Department of Biochemistry, Molecular and Cellular Biology, The University of Tennessee, Knoxville. 309 Ken and Blaire Mossman Bldg. 1311 Cumberland Avenue, Knoxville, TN 37996, United States
| | - Isabella Daidone
- Department of Physical and Chemical Sciences, University of L'Aquila, Via Vetoio, I-67010 L'Aquila, Italy
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46
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Devarajan D, Liang L, Gu B, Brooks SC, Parks JM, Smith JC. Molecular Dynamics Simulation of the Structures, Dynamics, and Aggregation of Dissolved Organic Matter. Environ Sci Technol 2020; 54:13527-13537. [PMID: 32985864 DOI: 10.1021/acs.est.0c01176] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Dissolved organic matter (DOM) plays a significant role in the transport and transformation of pollutants in the aquatic environment. However, the experimental characterization of DOM has been limited mainly to bulk properties, and the molecular-level interactions among various components of DOM remain to be fully characterized. Here, we use molecular dynamics (MD) simulations to probe the structural properties of model DOM systems at atomic detail. The 200 ns simulations, validated by available experimental data, reveal processes and mechanisms by which chemical species (cations, peptides, lipids, lignin, carbohydrates, and some low-molecular-weight aliphatic and aromatic compounds) aggregate to form complex DOM. The DOM aggregates are dynamic, consisting of a hydrophobic core and amphiphilic exterior. The lipid tails and other hydrophobic fragments form the core, with hydrophilic and amphiphilic groups exposed to water, making DOM accessible to both polar and nonpolar species. Thus, the lipid component acts as a nucleator, whereas cations (especially Ca2+) connect the molecular fragments on the surface by coordinating with the O-containing functional groups of DOM. The structural details revealed here provide new insights including surface accessible atoms, overall assemblage, and interactions among the molecules of DOM for understanding the kinetics and mechanisms through which DOM interacts with metal and other contaminants.
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Affiliation(s)
- Deepa Devarajan
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Liyuan Liang
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Earth and Planetary Sciences, University of Tennessee, Knoxville, Tennessee 37996, United States
| | - Baohua Gu
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Scott C Brooks
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6309, United States
| | - Jerry M Parks
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, Tennessee 37996, United States
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47
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Smith MD, Smith JC. Effects of sodium and calcium chloride ionic stresses on model yeast membranes revealed by molecular dynamics simulation. Chem Phys Lipids 2020; 233:104980. [PMID: 33038307 DOI: 10.1016/j.chemphyslip.2020.104980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/27/2020] [Accepted: 09/28/2020] [Indexed: 11/25/2022]
Abstract
As efforts to move a renewable economy grow, it will be necessary to make use of microbial conversion strategies for the production of novel materials or the upgrading of waste to high-value products. One critical technical challenge currently limiting waste upgrading remains the difficulty in obtaining single-pot conversion techniques where physical, chemical, and biological conversion are performed in a single step. To overcome this challenge, a detailed understanding of how different stresses impact microbial membrane stability will be necessary. Using all-atom molecular dynamics simulations, we examine the impacts of moderate concentrations of NaCl and CaCl2on a model yeast plasma membrane. Weak, though statistically significant, changes in membrane morphology and dynamics functions are observed that are consistent with swelling and stiffening. Additionally, an examination of the ion-lipid contacts and the behavior of water at the water-membrane interface suggests that the impacts of these common salts may, in part, be mediated through changes to water-membrane hydrogen-bonding and hydration water dynamics.
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Affiliation(s)
- Micholas Dean Smith
- Department of Biochemistry, Molecular & Cellular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, United States.
| | - Jeremy C Smith
- Department of Biochemistry, Molecular & Cellular Biology, The University of Tennessee, Knoxville, Knoxville, TN, United States; UT/ORNL Center for Molecular Biophysics, Oak Ridge, TN, United States
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48
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Ishida T, Parks JM, Smith JC. Insight into the Catalytic Mechanism of GH11 Xylanase: Computational Analysis of Substrate Distortion Based on a Neutron Structure. J Am Chem Soc 2020; 142:17966-17980. [PMID: 32959658 DOI: 10.1021/jacs.0c02148] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of biomass decomposition by xylanases remains the subject of debate. To clarify the mechanism we investigated the glycosylation step of GH11 xylanase, an enzyme that catalyzes the hydrolysis of lignocellulosic hemicellulose (xylan). Making use of a recent neutron crystal structure, which revealed the protonation states of relevant residues, we used ab initio quantum mechanics/molecular mechanics (QM/MM) calculations to determine the detailed reaction mechanism of the glycosylation step. In particular, our focus is on the controversial question of whether or not an oxocarbenium ion intermediate is formed on the reaction pathway. The calculations support the validity of a basic retaining mechanism within a double-displacement scheme. The estimated free energy barrier of this reaction is ∼18 kcal/mol with QM/MM-CCSD(T)/6-31(+)G**//MP2/6-31+G**/AMBER calculations, and the rate-determining step of the glycosylation is scission of the glycosidic bond after proton transfer from the acidic Glu177. The estimated lifetime of the oxocarbenium ion intermediate (on the order of tens of ps) and the secondary kinetic isotope effect suggest that there is no accumulation of this intermediate on the reaction path, although the intermediate can be transiently formed. In the enzyme-substrate (ES) complex, the carbohydrate structure of the xylose residue at the -1 subsite has a rather distorted (skewed) geometry, and this xylose unit at the active site has an apparent half-chair conformation when the oxocarbenium ion intermediate is formed. The major catalytic role of the protein environment is to orient residues that take part in the initial proton transfer. Because of a fine alignment of catalytic residues, the enzyme can accelerate the glycosylation reaction without paying a reorganization energy penalty.
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Affiliation(s)
- Toyokazu Ishida
- Research Center for Computational Design of Advanced Functional Materials (CD-FMat), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 2, 1-1-1 Umezono, Tsukuba 305-8568, Japan
| | - Jerry M Parks
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
| | - Jeremy C Smith
- Center for Molecular Biophysics (CMB), Biosciences Division, Oak Ridge National Laboratory (ORNL), 1 Bethel Valley Road, Oak Ridge, Tennessee 37831-6309, United States
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49
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Aranha MP, Jewel YSM, Beckman RA, Weiner LM, Mitchell JC, Parks JM, Smith JC. Combining Three-Dimensional Modeling with Artificial Intelligence to Increase Specificity and Precision in Peptide-MHC Binding Predictions. J Immunol 2020; 205:1962-1977. [PMID: 32878910 PMCID: PMC7511449 DOI: 10.4049/jimmunol.1900918] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/01/2020] [Indexed: 02/06/2023]
Abstract
The reliable prediction of the affinity of candidate peptides for the MHC is important for predicting their potential antigenicity and thus influences medical applications, such as decisions on their inclusion in T cell-based vaccines. In this study, we present a rapid, predictive computational approach that combines a popular, sequence-based artificial neural network method, NetMHCpan 4.0, with three-dimensional structural modeling. We find that the ensembles of bound peptide conformations generated by the programs MODELLER and Rosetta FlexPepDock are less variable in geometry for strong binders than for low-affinity peptides. In tests on 1271 peptide sequences for which the experimental dissociation constants of binding to the well-characterized murine MHC allele H-2Db are known, by applying thresholds for geometric fluctuations the structure-based approach in a standalone manner drastically improves the statistical specificity, reducing the number of false positives. Furthermore, filtering candidates generated with NetMHCpan 4.0 with the structure-based predictor led to an increase in the positive predictive value (PPV) of the peptides correctly predicted to bind very strongly (i.e., K d < 100 nM) from 40 to 52% (p = 0.027). The combined method also significantly improved the PPV when tested on five human alleles, including some with limited data for training. Overall, an average increase of 10% in the PPV was found over the standalone sequence-based method. The combined method should be useful in the rapid design of effective T cell-based vaccines.
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Affiliation(s)
- Michelle P Aranha
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Yead S M Jewel
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Robert A Beckman
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC 20007
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University Medical Center, Washington, DC 20007
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Louis M Weiner
- Department of Oncology and Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington, DC 20057
| | - Julie C Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Jerry M Parks
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830
| | - Jeremy C Smith
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37916;
- Center for Molecular Biophysics, Oak Ridge National Laboratory, Oak Ridge, TN 37830
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Gupta M, Ha K, Agarwal R, Quarles LD, Smith JC. Molecular dynamics analysis of the binding of human interleukin-6 with interleukin-6 α-receptor. Proteins 2020; 89:163-173. [PMID: 32881084 DOI: 10.1002/prot.26002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/26/2020] [Accepted: 08/25/2020] [Indexed: 11/07/2022]
Abstract
Human interleukin-6 (hIL-6) is a multifunctional cytokine that regulates immune and inflammatory responses in addition to metabolic and regenerative processes and cancer. hIL-6 binding to the IL-6 receptor (IL-6Rα) induces homodimerization and recruitment of the glycoprotein (gp130) to form a hexameric signaling complex. Anti-IL-6 and IL-6R antibodies are clinically approved inhibitors of IL-6 signaling pathway for treating rheumatoid arthritis and Castleman's disease, respectively. There is a potential to develop novel small molecule IL-6 antagonists derived from understanding the structural basis for IL-6/IL-6Rα interactions. Here, we combine homology modeling with extensive molecular dynamics (MD) simulations to examine the association of hIL-6 with IL-6Rα. A comparison with MD of apo hIL-6 reveals that the binding of hIL-6 to IL-6Rα induces structural and dynamic rearrangements in the AB loop region of hIL-6, disrupting intraprotein contacts and increasing the flexibility of residues 48 to 58 of the AB loop. In contrast, due to the involvement of residues 59 to 78 in forming contacts with the receptor, these residues of the AB loop are observed to rigidify in the presence of the receptor. The binary complex is primarily stabilized by two pairs of salt bridges, Arg181 (hIL-6)- Glu182 (IL-6Rα) and Arg184 (hIL-6)- Glu183 (IL-6Rα) as well as hydrophobic and aromatic stacking interactions mediated essentially by Phe residues in both proteins. An interplay of electrostatic, hydrophobic, hydrogen bonding, and aromatic stacking interactions facilitates the formation of the hIL-6/IL-6Rα complex.
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Affiliation(s)
- Madhulika Gupta
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - Khanh Ha
- Tickle College of Engineering, University of Tennessee, Knoxville, Tennessee, USA
| | - Rupesh Agarwal
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
| | - Leigh Darryl Quarles
- Division of Nephrology, University of Tennessee Health Science Center, Memphis, Tennessee, USA
| | - Jeremy C Smith
- UT/ORNL Center for Molecular Biophysics, Oak Ridge National Lab, Oak Ridge, Tennessee, USA
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