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Adcox HE, Hunt JR, Allen PE, Siff TE, Rodino KG, Ottens AK, Carlyon JA. Orientia tsutsugamushi Ank5 promotes NLRC5 cytoplasmic retention and degradation to inhibit MHC class I expression. Nat Commun 2024; 15:8069. [PMID: 39277599 PMCID: PMC11401901 DOI: 10.1038/s41467-024-52119-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 08/27/2024] [Indexed: 09/17/2024] Open
Abstract
How intracellular bacteria subvert the major histocompatibility complex (MHC) class I pathway is poorly understood. Here, we show that the obligate intracellular bacterium Orientia tsutsugamushi uses its effector protein, Ank5, to inhibit nuclear translocation of the MHC class I gene transactivator, NLRC5, and orchestrate its proteasomal degradation. Ank5 uses a tyrosine in its fourth ankyrin repeat to bind the NLRC5 N-terminus while its F-box directs host SCF complex ubiquitination of NLRC5 in the leucine-rich repeat region that dictates susceptibility to Orientia- and Ank5-mediated degradation. The ability of O. tsutsugamushi strains to degrade NLRC5 correlates with ank5 genomic carriage. Ectopically expressed Ank5 that can bind but not degrade NLRC5 protects the transactivator during Orientia infection. Thus, Ank5 is an immunoevasin that uses its bipartite architecture to rid host cells of NLRC5 and reduce surface MHC class I molecules. This study offers insight into how intracellular pathogens can impair MHC class I expression.
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Affiliation(s)
- Haley E Adcox
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, School of Medicine, Charlottesville, VA, USA
| | - Jason R Hunt
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
| | - Paige E Allen
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
| | - Thomas E Siff
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
| | - Kyle G Rodino
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Andrew K Ottens
- Department of Anatomy and Neurobiology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA
| | - Jason A Carlyon
- Department of Microbiology and Immunology, Virginia Commonwealth University Medical Center, School of Medicine, Richmond, VA, USA.
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2
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Dziadek ŁJ, Sieradzan AK, Czaplewski C, Zalewski M, Banaś F, Toczek M, Nisterenko W, Grudinin S, Liwo A, Giełdoń A. Assessment of Four Theoretical Approaches to Predict Protein Flexibility in the Crystal Phase and Solution. J Chem Theory Comput 2024; 20:7667-7681. [PMID: 39171852 PMCID: PMC11391579 DOI: 10.1021/acs.jctc.4c00754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
In this paper, we evaluated the ability of four coarse-grained methods to predict protein flexible regions with potential biological importance, UNRES-flex, UNRES-DSSP-flex (based on the united residue model of polypeptide chains without and with secondary structure restraints, respectively), CABS-flex (based on the C-α, C-β, and side chain model), and nonlinear rigid block normal mode analysis (NOLB) with a set of 100 protein structures determined by NMR spectroscopy or X-ray crystallography, with all secondary structure types. End regions with high fluctuations were excluded from analysis. The Pearson and Spearman correlation coefficients were used to quantify the conformity between the calculated and experimental fluctuation profiles, the latter determined from NMR ensembles and X-ray B-factors, respectively. For X-ray structures (corresponding to proteins in a crowded environment), NOLB resulted in the best agreement between the predicted and experimental fluctuation profiles, while for NMR structures (corresponding to proteins in solution), the ranking of performance is CABS-flex > UNRES-DSSP-flex > UNRES-flex > NOLB; however, CABS-flex sometimes exaggerated the extent of small fluctuations, as opposed to UNRES-DSSP-flex.
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Affiliation(s)
- Ł J Dziadek
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - A K Sieradzan
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - C Czaplewski
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
- School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, Seoul 02455, Republic of Korea
| | - M Zalewski
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - F Banaś
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - M Toczek
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - W Nisterenko
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - S Grudinin
- LJK, University Grenoble Alpes, CNRS, Grenoble INP, F-38000 Grenoble, France
| | - A Liwo
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
| | - A Giełdoń
- Faculty of Chemistry, University of Gdansk, ul. Wita-Stwosza 63, 80-308 Gdańsk, Poland
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3
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Christoffer C, Kihara D. Modeling protein-nucleic acid complexes with extremely large conformational changes using Flex-LZerD. Proteomics 2023; 23:e2200322. [PMID: 36529945 PMCID: PMC10448949 DOI: 10.1002/pmic.202200322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
Proteins and nucleic acids are key components in many processes in living cells, and interactions between proteins and nucleic acids are often crucial pathway components. In many cases, large flexibility of proteins as they interact with nucleic acids is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D atomic structures of such protein-nucleic acid complexes. When such structures are not yet experimentally determined, protein docking can be used to computationally generate useful structure models. However, such docking has long had the limitation that the consideration of flexibility is usually limited to small movements or to small structures. We previously developed a method of flexible protein docking which could model ordered proteins which undergo large-scale conformational changes, which we also showed was compatible with nucleic acids. Here, we elaborate on the ability of that pipeline, Flex-LZerD, to model specifically interactions between proteins and nucleic acids, and demonstrate that Flex-LZerD can model more interactions and types of conformational change than previously shown.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, Indiana, USA
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana, USA
- Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana, USA
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Lauro FV, Marcela RN, Maria LR, Francisco DC, Magdalena AR, Virginia MAM, Montserrat MG. Effect Produced by a Cyclooctyne Derivative on Both Infarct Area and Left Ventricular Pressure via Calcium Channel Activation. Drug Res (Stuttg) 2023; 73:105-112. [PMID: 36446591 DOI: 10.1055/a-1967-2004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
BACKGROUND There are reports which indicate that some cyclooctyne derivatives may exert changes in cardiovascular system; however, its molecular mechanism is not very clear. OBJECTIVE The aim of this study was to evaluate the biological activity of four cyclooctyne derivatives (compounds 1: to 4: ) produced on infarct area and left ventricular pressure. METHODS Biological activity produced by cyclooctyne derivatives on infarct area was determinate using an ischemia/reperfusion injury model. In addition, to characterize the molecular mechanism of this effect, the following strategies were carried out as follows; i) biological activity produced by cyclooctyne derivative (compound 4: ) on either perfusion pressure or left ventricular pressure was evaluated using an isolated rat heart; ii) theoretical interaction of cyclooctyne derivative with calcium channel (1t0j protein surface) using a docking model. RESULTS The results showed that cyclooctyne derivative (compound 4: ) decrease infarct area of in a dose-dependent manner compared with compound 1: to 3: . Besides, this cyclooctyne derivative increase both perfusion pressure and left ventricular pressure which was inhibited by nifedipine. Other theoretical data suggests that cyclooctyne derivative could interact with some aminoacid residues (Met83, Ile85, Ser86, Leu108, Glu114) involved in 1t0j protein surface. CONCLUSIONS All these data indicate that cyclooctyne derivative increase left ventricular pressure via calcium channel activation and this phenomenon could be translated as a decrease of infarct area.
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Affiliation(s)
- Figueroa-Valverde Lauro
- Laboratory of Pharmaco-Chemistry, Faculty of Chemical Biological Sciences, University Autonomous of Campeche, Av. Agustín Melgar s/n, Col Buenavista C.P. Campeche, Camp., México
| | - Rosas-Nexticapa Marcela
- Facultad de Nutrición, Universidad Veracruzana, Médicos y Odontologos s/n C.P. Unidad del Bosque Xalapa Veracruz, México
| | - López-Ramos Maria
- Laboratory of Pharmaco-Chemistry, Faculty of Chemical Biological Sciences, University Autonomous of Campeche, Av. Agustín Melgar s/n, Col Buenavista C.P. Campeche, Camp., México
| | - Díaz-Cedillo Francisco
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
| | - Alvarez-Ramirez Magdalena
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
| | - Mateu-Armad Maria Virginia
- Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional. Prol. Carpio y Plan de Ayala s/n Col. Santo Tomas, México, D.F. C.P
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Christoffer C, Kihara D. Domain-Based Protein Docking with Extremely Large Conformational Changes. J Mol Biol 2022; 434:167820. [PMID: 36089054 PMCID: PMC9992458 DOI: 10.1016/j.jmb.2022.167820] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 08/31/2022] [Accepted: 09/03/2022] [Indexed: 11/17/2022]
Abstract
Proteins are key components in many processes in living cells, and physical interactions with other proteins and nucleic acids often form key parts of their functions. In many cases, large flexibility of proteins as they interact is key to their function. To understand the mechanisms of these processes, it is necessary to consider the 3D structures of such protein complexes. When such structures are not yet experimentally determined, protein docking has long been present to computationally generate useful structure models. However, protein docking has long had the limitation that the consideration of flexibility is usually limited to very small movements or very small structures. Methods have been developed which handle minor flexibility via normal mode or other structure sampling, but new methods are required to model ordered proteins which undergo large-scale conformational changes to elucidate their function at the molecular level. Here, we present Flex-LZerD, a framework for docking such complexes. Via partial assembly multidomain docking and an iterative normal mode analysis admitting curvilinear motions, we demonstrate the ability to model the assembly of a variety of protein-protein and protein-nucleic acid complexes.
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Affiliation(s)
- Charles Christoffer
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, IN 47907, USA; Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA; Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA.
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6
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Varela D, Karlin V, André I. A memetic algorithm enables efficient local and global all-atom protein-protein docking with backbone and side-chain flexibility. Structure 2022; 30:1550-1558.e3. [DOI: 10.1016/j.str.2022.09.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 03/12/2022] [Accepted: 09/25/2022] [Indexed: 11/06/2022]
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7
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Karaca E, Prévost C, Sacquin-Mora S. Modeling the Dynamics of Protein-Protein Interfaces, How and Why? Molecules 2022; 27:1841. [PMID: 35335203 PMCID: PMC8950966 DOI: 10.3390/molecules27061841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 03/06/2022] [Accepted: 03/08/2022] [Indexed: 12/07/2022] Open
Abstract
Protein-protein assemblies act as a key component in numerous cellular processes. Their accurate modeling at the atomic level remains a challenge for structural biology. To address this challenge, several docking and a handful of deep learning methodologies focus on modeling protein-protein interfaces. Although the outcome of these methods has been assessed using static reference structures, more and more data point to the fact that the interaction stability and specificity is encoded in the dynamics of these interfaces. Therefore, this dynamics information must be taken into account when modeling and assessing protein interactions at the atomistic scale. Expanding on this, our review initially focuses on the recent computational strategies aiming at investigating protein-protein interfaces in a dynamic fashion using enhanced sampling, multi-scale modeling, and experimental data integration. Then, we discuss how interface dynamics report on the function of protein assemblies in globular complexes, in fuzzy complexes containing intrinsically disordered proteins, as well as in active complexes, where chemical reactions take place across the protein-protein interface.
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Affiliation(s)
- Ezgi Karaca
- Izmir Biomedicine and Genome Center, Izmir 35340, Turkey;
- Izmir International Biomedicine and Genome Institute, Dokuz Eylul University, Izmir 35340, Turkey
| | - Chantal Prévost
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
| | - Sophie Sacquin-Mora
- CNRS, Laboratoire de Biochimie Théorique, UPR9080, Université de Paris, 13 rue Pierre et Marie Curie, 75005 Paris, France;
- Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, PSL Research University, 75006 Paris, France
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8
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Faruk NF, Peng X, Freed KF, Roux B, Sosnick TR. Challenges and Advantages of Accounting for Backbone Flexibility in Prediction of Protein-Protein Complexes. J Chem Theory Comput 2022; 18:2016-2032. [PMID: 35213808 DOI: 10.1021/acs.jctc.1c01255] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Predicting protein binding is a core problem of computational biophysics. That this objective can be partly achieved with some amount of success using docking algorithms based on rigid protein models is remarkable, although going further requires allowing for protein flexibility. However, accurately capturing the conformational changes upon binding remains an enduring challenge for docking algorithms. Here, we adapt our Upside folding model, where side chains are represented as multi-position beads, to explore how flexibility may impact predictions of protein-protein complexes. Specifically, the Upside model is used to investigate where backbone flexibility helps, which types of interactions are important, and what is the impact of coarse graining. These efforts also shed light on the relative challenges posed by folding and docking. After training the Upside energy function for docking, the model is competitive with the established all-atom methods. However, allowing for backbone flexibility during docking is generally detrimental, as the presence of comparatively minor (3-5 Å) deviations relative to the docked structure has a large negative effect on performance. While this issue appears to be inherent to current forcefield-guided flexible docking methods, systems involving the co-folding of flexible loops such as antibody-antigen complexes represent an interesting exception. In this case, binding is improved when backbone flexibility is allowed using the Upside model.
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Affiliation(s)
- Nabil F Faruk
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, Illinois 60637, United States
| | - Xiangda Peng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States
| | - Karl F Freed
- Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States.,Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, United States.,Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois 60637, United States
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9
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Kurcinski M, Kmiecik S, Zalewski M, Kolinski A. Protein-Protein Docking with Large-Scale Backbone Flexibility Using Coarse-Grained Monte-Carlo Simulations. Int J Mol Sci 2021; 22:ijms22147341. [PMID: 34298961 PMCID: PMC8306105 DOI: 10.3390/ijms22147341] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 07/03/2021] [Accepted: 07/04/2021] [Indexed: 12/21/2022] Open
Abstract
Most of the protein–protein docking methods treat proteins as almost rigid objects. Only the side-chains flexibility is usually taken into account. The few approaches enabling docking with a flexible backbone typically work in two steps, in which the search for protein–protein orientations and structure flexibility are simulated separately. In this work, we propose a new straightforward approach for docking sampling. It consists of a single simulation step during which a protein undergoes large-scale backbone rearrangements, rotations, and translations. Simultaneously, the other protein exhibits small backbone fluctuations. Such extensive sampling was possible using the CABS coarse-grained protein model and Replica Exchange Monte Carlo dynamics at a reasonable computational cost. In our proof-of-concept simulations of 62 protein–protein complexes, we obtained acceptable quality models for a significant number of cases.
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10
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The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain. Int J Biol Macromol 2021; 186:54-70. [PMID: 34237360 DOI: 10.1016/j.ijbiomac.2021.06.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/20/2021] [Accepted: 06/29/2021] [Indexed: 11/20/2022]
Abstract
Lactoferrin (Lf), a bioactive milk protein, exhibits strong anticancer and antifungal activities. The search for Lf targets and mechanisms of action is of utmost importance to enhance its effective applications. A common feature among Lf-treated cancer and fungal cells is the inhibition of a proton pump called V-ATPase. Lf-driven V-ATPase inhibition leads to cytosolic acidification, ultimately causing cell death of cancer and fungal cells. Given that a detailed elucidation of how Lf and V-ATPase interact is still missing, herein we aimed to fill this gap by employing a five-stage computational approach. Molecular dynamics simulations of both proteins were performed to obtain a robust sampling of their conformational landscape, followed by clustering, which allowed retrieving representative structures, to then perform protein-protein docking. Subsequently, molecular dynamics simulations of the docked complexes and free binding energy calculations were carried out to evaluate the dynamic binding process and build a final ranking based on the binding affinities. Detailed atomist analysis of the top ranked complexes clearly indicates that Lf binds to the V1 cytosolic domain of V-ATPase. Particularly, our data suggest that Lf binds to the interfaces between A/B subunits, where the ATP hydrolysis occurs, thus inhibiting this process. The free energy decomposition analysis further identified key binding residues that will certainly aid in the rational design of follow-up experimental studies, hence bridging computational and experimental biochemistry.
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11
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Harmalkar A, Gray JJ. Advances to tackle backbone flexibility in protein docking. Curr Opin Struct Biol 2020; 67:178-186. [PMID: 33360497 DOI: 10.1016/j.sbi.2020.11.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/18/2020] [Accepted: 11/25/2020] [Indexed: 12/11/2022]
Abstract
Computational docking methods can provide structural models of protein-protein complexes, but protein backbone flexibility upon association often thwarts accurate predictions. In recent blind challenges, medium or high accuracy models were submitted in less than 20% of the 'difficult' targets (with significant backbone change or uncertainty). Here, we describe recent developments in protein-protein docking and highlight advances that tackle backbone flexibility. In molecular dynamics and Monte Carlo approaches, enhanced sampling techniques have reduced time-scale limitations. Internal coordinate formulations can now capture realistic motions of monomers and complexes using harmonic dynamics. And machine learning approaches adaptively guide docking trajectories or generate novel binding site predictions from deep neural networks trained on protein interfaces. These tools poise the field to break through the longstanding challenge of correctly predicting complex structures with significant conformational change.
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Affiliation(s)
- Ameya Harmalkar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Jeffrey J Gray
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Program in Molecular Biophysics, Institute for Nanobiotechnology, and Center for Computational Biology, Johns Hopkins University, Baltimore, MD, USA.
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12
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Torchala M, Gerguri T, Chaleil RAG, Gordon P, Russell F, Keshani M, Bates PA. Enhanced sampling of protein conformational states for dynamic cross-docking within the protein-protein docking server SwarmDock. Proteins 2020; 88:962-972. [PMID: 31697436 PMCID: PMC7496321 DOI: 10.1002/prot.25851] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 10/02/2019] [Accepted: 11/03/2019] [Indexed: 12/12/2022]
Abstract
The formation of specific protein-protein interactions is often a key to a protein's function. During complex formation, each protein component will undergo a change in the conformational state, for some these changes are relatively small and reside primarily at the sidechain level; however, others may display notable backbone adjustments. One of the classic problems in the protein-docking field is to be able to a priori predict the extent of such conformational changes. In this work, we investigated three protocols to find the most suitable input structure conformations for cross-docking, including a robust sampling approach in normal mode space. Counterintuitively, knowledge of the theoretically best combination of normal modes for unbound-bound transitions does not always lead to the best results. We used a novel spatial partitioning library, Aether Engine (see Supplementary Materials), to efficiently search the conformational states of 56 receptor/ligand pairs, including a recent CAPRI target, in a systematic manner and selected diverse conformations as input to our automated docking server, SwarmDock, a server that allows moderate conformational adjustments during the docking process. In essence, here we present a dynamic cross-docking protocol, which when benchmarked against the simpler approach of just docking the unbound components shows a 10% uplift in the quality of the top docking pose.
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Affiliation(s)
- Mieczyslaw Torchala
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
- Hadean Supercomputing LtdLondonUK
| | - Tereza Gerguri
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
| | | | | | | | | | - Paul A. Bates
- Biomolecular Modelling LaboratoryThe Francis Crick InstituteLondonUK
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