51
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Vishwanath S, Carnell GW, Ferrari M, Asbach B, Billmeier M, George C, Sans MS, Nadesalingam A, Huang CQ, Paloniemi M, Stewart H, Chan A, Wells DA, Neckermann P, Peterhoff D, Einhauser S, Cantoni D, Neto MM, Jordan I, Sandig V, Tonks P, Temperton N, Frost S, Sohr K, Ballesteros MTL, Arbabi F, Geiger J, Dohmen C, Plank C, Kinsley R, Wagner R, Heeney JL. A computationally designed antigen eliciting broad humoral responses against SARS-CoV-2 and related sarbecoviruses. Nat Biomed Eng 2023:10.1038/s41551-023-01094-2. [PMID: 37749309 DOI: 10.1038/s41551-023-01094-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 08/23/2023] [Indexed: 09/27/2023]
Abstract
The threat of spillovers of coronaviruses associated with the severe acute respiratory syndrome (SARS) from animals to humans necessitates vaccines that offer broader protection from sarbecoviruses. By leveraging a viral-genome-informed computational method for selecting immune-optimized and structurally engineered antigens, here we show that a single antigen based on the receptor binding domain of the spike protein of sarbecoviruses elicits broad humoral responses against SARS-CoV-1, SARS-CoV-2, WIV16 and RaTG13 in mice, rabbits and guinea pigs. When administered as a DNA immunogen or by a vector based on a modified vaccinia virus Ankara, the optimized antigen induced vaccine protection from the Delta variant of SARS-CoV-2 in mice genetically engineered to express angiotensin-converting enzyme 2 and primed by a viral-vector vaccine (AZD1222) against SARS-CoV-2. A vaccine formulation incorporating mRNA coding for the optimized antigen further validated its broad immunogenicity. Vaccines that elicit broad immune responses across subgroups of coronaviruses may counteract the threat of zoonotic spillovers of betacoronaviruses.
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Affiliation(s)
- Sneha Vishwanath
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - George William Carnell
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Benedikt Asbach
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Martina Billmeier
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Charlotte George
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Maria Suau Sans
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Angalee Nadesalingam
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Chloe Qingzhou Huang
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Minna Paloniemi
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Hazel Stewart
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Andrew Chan
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | | | - Patrick Neckermann
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - David Peterhoff
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Sebastian Einhauser
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
| | - Diego Cantoni
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | - Martin Mayora Neto
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | | | | | - Paul Tonks
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham, UK
| | - Simon Frost
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
- London School of Hygiene and Tropical Medicine, London, UK
- Microsoft Health Futures, Redmond, WA, USA
| | | | | | | | | | | | | | - Rebecca Kinsley
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
| | - Ralf Wagner
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK
- Institute of Medical Microbiology and Hygiene, University of Regensburg, Regensburg, Germany
- Institute of Clinical Microbiology and Hygiene, University Hospital Regensburg, Regensburg, Germany
| | - Jonathan Luke Heeney
- Lab of Viral Zoonotics, Department of Veterinary Medicine, University of Cambridge, Cambridge, UK.
- DIOSynVax Ltd, University of Cambridge, Cambridge, UK.
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52
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Gaudreault F, Corbeil CR, Sulea T. Enhanced antibody-antigen structure prediction from molecular docking using AlphaFold2. Sci Rep 2023; 13:15107. [PMID: 37704686 PMCID: PMC10499836 DOI: 10.1038/s41598-023-42090-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 09/05/2023] [Indexed: 09/15/2023] Open
Abstract
Predicting the structure of antibody-antigen complexes has tremendous value in biomedical research but unfortunately suffers from a poor performance in real-life applications. AlphaFold2 (AF2) has provided renewed hope for improvements in the field of protein-protein docking but has shown limited success against antibody-antigen complexes due to the lack of co-evolutionary constraints. In this study, we used physics-based protein docking methods for building decoy sets consisting of low-energy docking solutions that were either geometrically close to the native structure (positives) or not (negatives). The docking models were then fed into AF2 to assess their confidence with a novel composite score based on normalized pLDDT and pTMscore metrics after AF2 structural refinement. We show benefits of the AF2 composite score for rescoring docking poses both in terms of (1) classification of positives/negatives and of (2) success rates with particular emphasis on early enrichment. Docking models of at least medium quality present in the decoy set, but not necessarily highly ranked by docking methods, benefitted most from AF2 rescoring by experiencing large advances towards the top of the reranked list of models. These improvements, obtained without any calibration or novel methodologies, led to a notable level of performance in antibody-antigen unbound docking that was never achieved previously.
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Affiliation(s)
- Francis Gaudreault
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Christopher R Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, 6100 Royalmount Avenue, Montreal, QC, H4P 2R2, Canada.
- Institute of Parasitology, McGill University, 21111 Lakeshore Road, Sainte-Anne-de-Bellevue, QC, H9X 3V9, Canada.
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53
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Alshahrani M, Gupta G, Xiao S, Tao P, Verkhivker G. Examining Functional Linkages Between Conformational Dynamics, Protein Stability and Evolution of Cryptic Binding Pockets in the SARS-CoV-2 Omicron Spike Complexes with the ACE2 Host Receptor: Recombinant Omicron Variants Mediate Variability of Conserved Allosteric Sites and Binding Epitopes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.11.557205. [PMID: 37745525 PMCID: PMC10515794 DOI: 10.1101/2023.09.11.557205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full length trimer complexes with the ACE2 receptor complemented atomistic studies and enabled an in-depth analysis of mutational and binding effects on conformational dynamic and functional adaptability of the Omicron variants. Despite considerable structural similarities, Omicron variants BA.2, BA.2.75 and XBB.1 can induce unique conformational dynamic signatures and specific distributions of the conformational states. Using conformational ensembles of the SARS-CoV-2 Omicron spike trimer complexes with ACE2, we conducted a comprehensive cryptic pocket screening to examine the role of Omicron mutations and ACE2 binding on the distribution and functional mechanisms of the emerging allosteric binding sites. This analysis captured all experimentally known allosteric sites and discovered networks of inter-connected and functionally relevant allosteric sites that are governed by variant-sensitive conformational adaptability of the SARS-CoV-2 spike structures. The results detailed how ACE2 binding and Omicron mutations in the BA.2, BA.2.75 and XBB.1 spike complexes modulate the distribution of conserved and druggable allosteric pockets harboring functionally important regions. The results of are significant for understanding functional roles of druggable cryptic pockets that can be used for allostery-mediated therapeutic intervention targeting conformational states of the Omicron variants.
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54
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Shao Q, Jiang Y, Yang ZJ. EnzyHTP Computational Directed Evolution with Adaptive Resource Allocation. J Chem Inf Model 2023; 63:5650-5659. [PMID: 37611241 PMCID: PMC11211066 DOI: 10.1021/acs.jcim.3c00618] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/25/2023]
Abstract
Directed evolution facilitates enzyme engineering via iterative rounds of mutagenesis. Despite the wide applications of high-throughput screening, building "smart libraries" to effectively identify beneficial variants remains a major challenge in the community. Here, we developed a new computational directed evolution protocol based on EnzyHTP, a software that we have previously reported to automate enzyme modeling. To enhance the throughput efficiency, we implemented an adaptive resource allocation strategy that dynamically allocates different types of computing resources (e.g., GPU/CPU) based on the specific need of an enzyme modeling subtask in the workflow. We implemented the strategy as a Python library and tested the library using fluoroacetate dehalogenase as a model enzyme. The results show that compared to fixed resource allocation where both CPU and GPU are on-call for use during the entire workflow, applying adaptive resource allocation can save 87% CPU hours and 14% GPU hours. Furthermore, we constructed a computational directed evolution protocol under the framework of adaptive resource allocation. The workflow was tested against two rounds of mutational screening in the directed evolution experiments of Kemp eliminase (KE07) with a total of 184 mutants. Using folding stability and electrostatic stabilization energy as computational readout, we identified all four experimentally observed target variants. Enabled by the workflow, the entire computation task (i.e., 18.4 μs MD and 18,400 QM single-point calculations) completes in 3 days of wall-clock time using ∼30 GPUs and ∼1000 CPUs.
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Affiliation(s)
- Qianzhen Shao
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Yaoyukun Jiang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Zhongyue J. Yang
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Center for Structural Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University, Nashville, Tennessee 37235, United States
- Data Science Institute, Vanderbilt University, Nashville, Tennessee 37235, United States
- Department of Chemical and Biomolecular Engineering, Vanderbilt University, Nashville, Tennessee 37235, United States
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55
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von Beck T, Navarrete K, Arce NA, Gao M, Dale GA, Davis-Gardner ME, Floyd K, Mena Hernandez L, Mullick N, Vanderheiden A, Skountzou I, Kuchipudi SV, Saravanan R, Li R, Skolnick J, Suthar MS, Jacob J. A wild boar cathelicidin peptide derivative inhibits severe acute respiratory syndrome coronavirus-2 and its drifted variants. Sci Rep 2023; 13:14650. [PMID: 37670110 PMCID: PMC10480232 DOI: 10.1038/s41598-023-41850-7] [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: 12/22/2022] [Accepted: 08/31/2023] [Indexed: 09/07/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) poses a clear threat to humanity. It has infected over 200 million and killed 4 million people worldwide, and infections continue with no end in sight. To control the pandemic, multiple effective vaccines have been developed, and global vaccinations are in progress. However, the virus continues to mutate. Even when full vaccine coverage is achieved, vaccine-resistant mutants will likely emerge, thus requiring new annual vaccines against drifted variants analogous to influenza. A complimentary solution to this problem could be developing antiviral drugs that inhibit SARS CoV-2 and its drifted variants. Host defense peptides represent a potential source for such an antiviral as they possess broad antimicrobial activity and significant diversity across species. We screened the cathelicidin family of peptides from 16 different species for antiviral activity and identified a wild boar peptide derivative that inhibits SARS CoV-2. This peptide, which we named Yongshi and means warrior in Mandarin, acts as a viral entry inhibitor. Following the binding of SARS-CoV-2 to its receptor, the spike protein is cleaved, and heptad repeats 1 and 2 multimerize to form the fusion complex that enables the virion to enter the cell. A deep learning-based protein sequence comparison algorithm and molecular modeling suggest that Yongshi acts as a mimetic to the heptad repeats of the virus, thereby disrupting the fusion process. Experimental data confirm the binding of Yongshi to the heptad repeat 1 with a fourfold higher affinity than heptad repeat 2 of SARS-CoV-2. Yongshi also binds to the heptad repeat 1 of SARS-CoV-1 and MERS-CoV. Interestingly, it inhibits all drifted variants of SARS CoV-2 that we tested, including the alpha, beta, gamma, delta, kappa and omicron variants.
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Affiliation(s)
- Troy von Beck
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Karla Navarrete
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Nicholas A Arce
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Mu Gao
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, GA, 30332, USA
| | - Gordon A Dale
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Meredith E Davis-Gardner
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Katharine Floyd
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Luis Mena Hernandez
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Nikita Mullick
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Abigail Vanderheiden
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Ioanna Skountzou
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
| | - Suresh V Kuchipudi
- Animal Diagnostic Laboratory, Department of Veterinary and Biomedical Sciences, The Center for Infectious Disease Dynamics, Pennsylvania State University, University Park, PA, 16802, USA
| | - Rathi Saravanan
- Centre of Regulatory Excellence (CoRE), Duke-NUS Medical School, Level 6, 8 College Road, Singapore, 169857, Singapore
| | - Renhao Li
- Department of Pediatrics, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, 950 Atlantic Drive, NW, Atlanta, GA, 30332, USA
| | - Mehul S Suthar
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA
- Division of Infectious Diseases, Department of Pediatrics, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Joshy Jacob
- Emory Vaccine Center, Emory National Primate Research Center, Emory University, 954 Gatewood Road, Atlanta, GA, 30329, USA.
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56
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Opuu V, Nigro G, Lazennec‐Schurdevin C, Mechulam Y, Schmitt E, Simonson T. Redesigning methionyl-tRNA synthetase for β-methionine activity with adaptive landscape flattening and experiments. Protein Sci 2023; 32:e4738. [PMID: 37518893 PMCID: PMC10451022 DOI: 10.1002/pro.4738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/21/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023]
Abstract
Amino acids (AAs) with a noncanonical backbone would be a valuable tool for protein engineering, enabling new structural motifs and building blocks. To incorporate them into an expanded genetic code, the first, key step is to obtain an appropriate aminoacyl-tRNA synthetase. Currently, directed evolution is not available to optimize AAs with noncanonical backbones, since an appropriate selective pressure has not been discovered. Computational protein design (CPD) is an alternative. We used a new CPD method to redesign MetRS and increase its activity towards β-Met, which has an extra backbone methylene. The new method considered a few active site positions for design and used a Monte Carlo exploration of the corresponding sequence space. During the exploration, a bias energy was adaptively learned, such that the free energy landscape of the apo enzyme was flattened. Enzyme variants could then be sampled, in the presence of the ligand and the bias energy, according to their β-Met binding affinities. Eighteen predicted variants were chosen for experimental testing; 10 exhibited detectable activity for β-Met adenylation. Top predicted hits were characterized experimentally in detail. Dissociation constants, catalytic rates, and Michaelis constants for both α-Met and β-Met were measured. The best mutant retained a preference for α-Met over β-Met; however, the preference was reduced, compared to the wildtype, by a factor of 29. For this mutant, high resolution crystal structures were obtained in complex with both α-Met and β-Met, indicating that the predicted, active conformation of β-Met in the active site was retained.
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Affiliation(s)
- Vaitea Opuu
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Giuliano Nigro
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Christine Lazennec‐Schurdevin
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Yves Mechulam
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Emmanuelle Schmitt
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
| | - Thomas Simonson
- Laboratoire de Biologie Structurale de la Cellule (CNRS UMR7654), Ecole PolytechniqueInstitut Polytechnique de ParisPalaiseauFrance
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57
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Mirzaei R, Shafiee S, Vafaei R, Salehi M, Jalili N, Nazerian Z, Muhammadnajad A, Yadegari F, Reza Esmailinejad M, Farahmand L. Production of novel recombinant anti-EpCAM antibody as targeted therapy for breast cancer. Int Immunopharmacol 2023; 122:110656. [PMID: 37473710 DOI: 10.1016/j.intimp.2023.110656] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 07/10/2023] [Accepted: 07/13/2023] [Indexed: 07/22/2023]
Abstract
BACKGROUND The utilization of monoclonal antibodies (moAbs), an issue correlated with the biopharmaceutical professions, is developing and maturing. Coordinated with this conception, we produced the appealingly modeled anti-EpCAM scFv for breast cancer tumors. METHODS Afterward cloning and expression of recombinant antibody in Escherichia coli bacteria, the correctness of the desired antibody was checked by western blotting. Flow cytometry was utilized to determine the capacity of the recombinant antibody to append to the desired receptors in the malignant breast cancer (BC)cell line. The recombinant antibody (anti-EpCAM scFv) was examined for preclinical efficacy in reducing tumor growth, angiogenesis, and invasiveness (in vitro- in vivo). FINDINGS A target antibody-mediated attenuation of migration and invasion in the examined cancer cell lines was substantiated (P-value < 0.05). Grafted tumors from breast cancer in mice indicated significant and compelling suppression of tumor growth and decrement in blood supply in reaction to the recombinant anti-EpCAM intervention. Evaluations of immunohistochemical and histopathological findings revealed an enhanced response rate to the treatment. CONCLUSION The desired anti-EpCAM scFv can be a therapeutic tool to reduce invasion and proliferation in malignant breast cancer.
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Affiliation(s)
- Roya Mirzaei
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Soodabeh Shafiee
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Rana Vafaei
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran; Department of Surgery and Radiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Malihe Salehi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Neda Jalili
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Zahra Nazerian
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Ahad Muhammadnajad
- Cancer Biology Research Center, Cancer Institute of Iran, Tehran University of Medical Sciences, Tehran, Iran
| | - Fatemeh Yadegari
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Mohamad Reza Esmailinejad
- Department of Surgery and Radiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Leila Farahmand
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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58
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Petrovskiy DV, Nikolsky KS, Rudnev VR, Kulikova LI, Butkova TV, Malsagova KA, Kopylov AT, Kaysheva AL. Modeling Side Chains in the Three-Dimensional Structure of Proteins for Post-Translational Modifications. Int J Mol Sci 2023; 24:13431. [PMID: 37686234 PMCID: PMC10488155 DOI: 10.3390/ijms241713431] [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: 08/08/2023] [Revised: 08/23/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Amino acid substitutions and post-translational modifications (PTMs) play a crucial role in many cellular processes by directly affecting the structural and dynamic features of protein interaction. Despite their importance, the understanding of protein PTMs at the structural level is still largely incomplete. The Protein Data Bank contains a relatively small number of 3D structures having post-translational modifications. Although recent years have witnessed significant progress in three-dimensional modeling (3D) of proteins using neural networks, the problem related to predicting accurate PTMs in proteins has been largely ignored. Predicting accurate 3D PTM models in proteins is closely related to another fundamental problem: predicting the correct side-chain conformations of amino acid residues in proteins. An analysis of publications as well as the paid and free software packages for modeling three-dimensional structures showed that most of them focus on working with unmodified proteins and canonical amino acid residues; the number of articles and software packages placing emphasis on modeling three-dimensional PTM structures is an order of magnitude smaller. This paper focuses on modeling the side-chain conformations of proteins containing PTMs (nonstandard amino acid residues). We collected our own libraries comprising the most frequently observed PTMs from the PDB and implemented a number of algorithms for predicting the side-chain conformation at modification points and in the immediate environment of the protein. A comprehensive analysis of both the algorithms per se and compared to the common Rosetta and FoldX structure modeling packages was also carried out. The proposed algorithmic solutions are comparable in their characteristics to the well-known Rosetta and FoldX packages for the modeling of three-dimensional structures and have great potential for further development and optimization. The source code of algorithmic solutions has been deposited to and is available at the GitHub source.
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Affiliation(s)
| | | | | | | | | | - Kristina A. Malsagova
- Institute of Biomedical Chemistry, 119121 Moscow, Russia; (D.V.P.); (K.S.N.); (V.R.R.); (L.I.K.); (T.V.B.); (A.T.K.); (A.L.K.)
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59
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Wei W, Hogues H, Sulea T. Comparative Performance of High-Throughput Methods for Protein p Ka Predictions. J Chem Inf Model 2023; 63:5169-5181. [PMID: 37549424 PMCID: PMC10466379 DOI: 10.1021/acs.jcim.3c00165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Indexed: 08/09/2023]
Abstract
The medically relevant field of protein-based therapeutics has triggered a demand for protein engineering in different pH environments of biological relevance. In silico engineering workflows typically employ high-throughput screening campaigns that require evaluating large sets of protein residues and point mutations by fast yet accurate computational algorithms. While several high-throughput pKa prediction methods exist, their accuracies are unclear due to the lack of a current comprehensive benchmarking. Here, seven fast, efficient, and accessible approaches including PROPKA3, DeepKa, PKAI, PKAI+, DelPhiPKa, MCCE2, and H++ were systematically tested on a nonredundant subset of 408 measured protein residue pKa shifts from the pKa database (PKAD). While no method outperformed the null hypotheses with confidence, as illustrated by statistical bootstrapping, DeepKa, PKAI+, PROPKA3, and H++ had utility. More specifically, DeepKa consistently performed well in tests across multiple and individual amino acid residue types, as reflected by lower errors, higher correlations, and improved classifications. Arithmetic averaging of the best empirical predictors into simple consensuses improved overall transferability and accuracy up to a root-mean-square error of 0.76 pKa units and a correlation coefficient (R2) of 0.45 to experimental pKa shifts. This analysis should provide a basis for further methodological developments and guide future applications, which require embedding of computationally inexpensive pKa prediction methods, such as the optimization of antibodies for pH-dependent antigen binding.
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Affiliation(s)
- Wanlei Wei
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Hervé Hogues
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
| | - Traian Sulea
- Human Health Therapeutics
Research Centre, National Research Council
Canada, 6100 Royalmount Avenue, Montreal, Quebec H4P 2R2, Canada
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60
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variant Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. J Chem Inf Model 2023; 63:5272-5296. [PMID: 37549201 PMCID: PMC11162552 DOI: 10.1021/acs.jcim.3c00778] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, microsecond molecular dynamics simulations, and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the functional conformational states and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant, which can be contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of the conformational states. The results suggested that variant-specific changes of the conformational mobility in the functional interfacial loops of the receptor-binding domain in the SARS-CoV-2 spike protein can be fine-tuned through crosstalk between convergent mutations which could provide an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulation of conformational plasticity and regulation of allosteric communications. This study also revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions.
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Affiliation(s)
- Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas 75275, United States
| | - Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, California 92866, United States
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, California 92618, United States
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61
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Maiti S, Heyden M. Model-Dependent Solvation of the K-18 Domain of the Intrinsically Disordered Protein Tau. J Phys Chem B 2023; 127:7220-7230. [PMID: 37556237 DOI: 10.1021/acs.jpcb.3c01726] [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: 08/11/2023]
Abstract
A known imbalance between intra-protein and protein-water interactions in many empirical force fields results in collapsed conformational ensembles of intrinsically disordered proteins in explicit solvent simulations that disagree with experiments. Multiple strategies have been introduced in the literature to modify protein-water interactions, which improve agreement between experiments and simulations. In this work, we combine simulations with standard and modified force fields with a spatially resolved analysis of solvation free energy contributions and compare the consequences of each strategy. We find that enhanced Lennard-Jones (LJ) interactions between protein atoms and water oxygens primarily improve the solvation of nonpolar functional groups of the protein. In contrast, modified electrostatics in the water model or strengthened LJ interactions between the protein and water hydrogens mainly affect the hydration of polar functional groups. Modified electrostatics further impact the average orientation of water molecules in the hydration shell. As a result, protein-water interactions with the first hydration layers are strengthened, while interactions with water molecules in higher hydration shells are weakened. Hence, distinct strategies to balance intra-protein and protein-water interactions in simulations have qualitatively different effects on protein solvation. These differences are not necessarily captured by comparisons to experiments that report on global parameters describing protein conformational ensembles, e.g., the radius of gyration, but will influence the tendency of a protein to form aggregates or phase-separated droplets.
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Affiliation(s)
- Sthitadhi Maiti
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
| | - Matthias Heyden
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85287, United States
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Gaudreault F, Baardsnes J, Martynova Y, Dachon A, Hogues H, Corbeil CR, Purisima EO, Arbour M, Sulea T. Exploring rigid-backbone protein docking in biologics discovery: a test using the DARPin scaffold. Front Mol Biosci 2023; 10:1253689. [PMID: 37692063 PMCID: PMC10484509 DOI: 10.3389/fmolb.2023.1253689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Accepted: 08/14/2023] [Indexed: 09/12/2023] Open
Abstract
Accurate protein-protein docking remains challenging, especially for artificial biologics not coevolved naturally against their protein targets, like antibodies and other engineered scaffolds. We previously developed ProPOSE, an exhaustive docker with full atomistic details, which delivers cutting-edge performance by allowing side-chain rearrangements upon docking. However, extensive protein backbone flexibility limits its practical applicability as indicated by unbound docking tests. To explore the usefulness of ProPOSE on systems with limited backbone flexibility, here we tested the engineered scaffold DARPin, which is characterized by its relatively rigid protein backbone. A prospective screening campaign was undertaken, in which sequence-diversified DARPins were docked and ranked against a directed epitope on the target protein BCL-W. In this proof-of-concept study, only a relatively small set of 2,213 diverse DARPin interfaces were selected for docking from the huge theoretical library from mutating 18 amino-acid positions. A computational selection protocol was then applied for enrichment of binders based on normalized computed binding scores and frequency of binding modes against the predefined epitope. The top-ranked 18 designed DARPin interfaces were selected for experimental validation. Three designs exhibited binding affinities to BCL-W in the nanomolar range comparable to control interfaces adopted from known DARPin binders. This result is encouraging for future screening and engineering campaigns of DARPins and possibly other similarly rigid scaffolds against targeted protein epitopes. Method limitations are discussed and directions for future refinements are proposed.
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Affiliation(s)
- Francis Gaudreault
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Jason Baardsnes
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Yuliya Martynova
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Aurore Dachon
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Hervé Hogues
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Christopher R. Corbeil
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Enrico O. Purisima
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Mélanie Arbour
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council Canada, Montreal, QC, Canada
- Institute of Parasitology, McGill University, Montreal, QC, Canada
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63
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Guarra F, Colombo G. Computational Methods in Immunology and Vaccinology: Design and Development of Antibodies and Immunogens. J Chem Theory Comput 2023; 19:5315-5333. [PMID: 37527403 PMCID: PMC10448727 DOI: 10.1021/acs.jctc.3c00513] [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: 05/17/2023] [Indexed: 08/03/2023]
Abstract
The design of new biomolecules able to harness immune mechanisms for the treatment of diseases is a prime challenge for computational and simulative approaches. For instance, in recent years, antibodies have emerged as an important class of therapeutics against a spectrum of pathologies. In cancer, immune-inspired approaches are witnessing a surge thanks to a better understanding of tumor-associated antigens and the mechanisms of their engagement or evasion from the human immune system. Here, we provide a summary of the main state-of-the-art computational approaches that are used to design antibodies and antigens, and in parallel, we review key methodologies for epitope identification for both B- and T-cell mediated responses. A special focus is devoted to the description of structure- and physics-based models, privileged over purely sequence-based approaches. We discuss the implications of novel methods in engineering biomolecules with tailored immunological properties for possible therapeutic uses. Finally, we highlight the extraordinary challenges and opportunities presented by the possible integration of structure- and physics-based methods with emerging Artificial Intelligence technologies for the prediction and design of novel antigens, epitopes, and antibodies.
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Affiliation(s)
- Federica Guarra
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
| | - Giorgio Colombo
- Department of Chemistry, University
of Pavia, Via Taramelli 12, 27100 Pavia, Italy
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64
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Huang SH, Chen YT, Lin XY, Ly YY, Lien ST, Chen PH, Wang CT, Wu SC, Chen CC, Lin CY. In silico prediction of immune-escaping hot spots for future COVID-19 vaccine design. Sci Rep 2023; 13:13468. [PMID: 37596329 PMCID: PMC10439115 DOI: 10.1038/s41598-023-40741-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/16/2023] [Indexed: 08/20/2023] Open
Abstract
The COVID-19 pandemic has had a widespread impact on a global scale, and the evolution of considerable dominants has already taken place. Some variants contained certain key mutations located on the receptor binding domain (RBD) of spike protein, such as E484K and N501Y. It is increasingly worrying that these variants could impair the efficacy of current vaccines or therapies. Therefore, analyzing and predicting the high-risk mutations of SARS-CoV-2 spike glycoprotein is crucial to design future vaccines against the different variants. In this work, we proposed an in silico approach, immune-escaping score (IES), to predict high-risk immune-escaping hot spots on the receptor-binding domain (RBD), implemented through integrated delta binding free energy measured by computational mutagenesis of spike-antibody complexes and mutation frequency calculated from viral genome sequencing data. We identified 23 potentially immune-escaping mutations on the RBD by using IES, nine of which occurred in omicron variants (R346K, K417N, N440K, L452Q, L452R, S477N, T478K, F490S, and N501Y), despite our dataset being curated before the omicron first appeared. The highest immune-escaping score (IES = 1) was found for E484K, which agrees with recent studies stating that the mutation significantly reduced the efficacy of neutralization antibodies. Furthermore, our predicted delta binding free energy and IES show a high correlation with high-throughput deep mutational scanning data (Pearson's r = 0.70) and experimentally measured neutralization titers data (mean Pearson's r = -0.80). In summary, our work presents a new method to identify the potentially immune-escaping mutations on the RBD and provides valuable insights into future COVID-19 vaccine design.
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Affiliation(s)
| | | | | | - Yi-Yi Ly
- Graphen Inc., New York, NY, 10110, USA
| | | | | | | | - Suh-Chin Wu
- Adimmune Corp., Taichung City, 427003, Taiwan
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65
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing conformational landscapes of binding and allostery in the SARS-CoV-2 omicron variant complexes using microsecond atomistic simulations and perturbation-based profiling approaches: hidden role of omicron mutations as modulators of allosteric signaling and epistatic relationships. Phys Chem Chem Phys 2023; 25:21245-21266. [PMID: 37548589 PMCID: PMC10536792 DOI: 10.1039/d3cp02042h] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 spike protein complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which can be contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using the dynamics-based mutational scanning of spike residues, we identified structural stability and binding affinity hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron mutations on allosteric interactions and communications in the complexes. The results of this analysis revealed specific roles of Omicron mutations as conformationally plastic and evolutionary adaptable modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes performed in the background of the original strain, we characterized regions of epistatic couplings that are centered around the binding affinity hotspots N501Y and Q498R. Our results dissected the vital role of these epistatic centers in regulating protein stability, efficient ACE2 binding and allostery which allows for accumulation of multiple Omicron immune escape mutations at other sites. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA.
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92093, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Grace Gupta
- Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA.
| | - Sian Xiao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
| | - Peng Tao
- Department of Chemistry, Center for Research Computing, Center for Drug Discovery, Design, and Delivery (CD4), Southern Methodist University, Dallas, Texas, 75275, USA.
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66
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Aina A, Hsueh SCC, Gibbs E, Peng X, Cashman NR, Plotkin SS. De Novo Design of a β-Helix Tau Protein Scaffold: An Oligomer-Selective Vaccine Immunogen Candidate for Alzheimer's Disease. ACS Chem Neurosci 2023; 14:2603-2617. [PMID: 37458595 DOI: 10.1021/acschemneuro.3c00007] [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] [Indexed: 08/03/2023] Open
Abstract
Tau pathology is associated with many neurodegenerative disorders, including Alzheimer's disease (AD), where the spatio-temporal pattern of tau neurofibrillary tangles strongly correlates with disease progression, which motivates therapeutics selective for misfolded tau. Here, we introduce a new avidity-enhanced, multi-epitope approach for protein-misfolding immunogen design, which is predicted to mimic the conformational state of an exposed epitope in toxic tau oligomers. A predicted oligomer-selective tau epitope 343KLDFK347 was scaffolded by designing a β-helix structure that incorporated multiple instances of the 16-residue tau fragment 339VKSEKLDFKDRVQSKI354. Large-scale conformational ensemble analyses involving Jensen-Shannon Divergence and the embedding depth D showed that the multi-epitope scaffolding approach, employed in designing the β-helix scaffold, was predicted to better discriminate toxic tau oligomers than other "monovalent" strategies utilizing a single instance of an epitope for vaccine immunogen design. Using Rosetta, 10,000 sequences were designed and screened for the linker portions of the β-helix scaffold, along with a C-terminal stabilizing α-helix that interacts with the linkers, to optimize the folded structure and stability of the scaffold. Structures were ranked by energy, and the lowest 1% (82 unique sequences) were verified using AlphaFold. Several selection criteria involving AlphaFold are implemented to obtain a lead-designed sequence. The structure was further predicted to have free energetic stability by using Hamiltonian replica exchange molecular dynamics (MD) simulations. The synthesized β-helix scaffold showed direct binding in surface plasmon resonance (SPR) experiments to several antibodies that were raised to the structured epitope using a designed cyclic peptide. Moreover, the strength of binding of these antibodies to in vitro tau oligomers correlated with the strength of binding to the β-helix construct, suggesting that the construct presents an oligomer-like conformation and may thus constitute an effective oligomer-selective immunogen.
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Affiliation(s)
- Adekunle Aina
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Shawn C C Hsueh
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Ebrima Gibbs
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Xubiao Peng
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Neil R Cashman
- Djavad Mowafaghian Centre for Brain Health, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven S Plotkin
- Department of Physics and Astronomy, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, The University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
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67
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Wongkittichote P, Duque Lasio ML, Magistrati M, Pathak S, Sample B, Carvalho DR, Ortega AB, Castro MAA, de Gusmao CM, Toler TL, Bellacchio E, Dallabona C, Shinawi M. Phenotypic, molecular, and functional characterization of COQ7-related primary CoQ 10 deficiency: Hypomorphic variants and two distinct disease entities. Mol Genet Metab 2023; 139:107630. [PMID: 37392700 PMCID: PMC10995746 DOI: 10.1016/j.ymgme.2023.107630] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/19/2023] [Accepted: 06/20/2023] [Indexed: 07/03/2023]
Abstract
Primary coenzyme Q10 (CoQ10) deficiency is a group of inborn errors of metabolism caused by defects in CoQ10 biosynthesis. Biallelic pathogenic variants in COQ7, encoding mitochondrial 5-demethoxyubiquinone hydroxylase, have been reported in nine patients from seven families. We identified five new patients with COQ7-related primary CoQ10 deficiency, performed clinical assessment of the patients, and studied the functional effects of current and previously reported COQ7 variants and potential treatment options. The main clinical features included a neonatal-onset presentation with severe neuromuscular, cardiorespiratory and renal involvement and a late-onset disease presenting with progressive neuropathy, lower extremity weakness, abnormal gait, and variable developmental delay. Baker's yeast orthologue of COQ7, CAT5, is required for growth on oxidative carbon sources and cat5Δ strain demonstrates oxidative growth defect. Expression of wild-type CAT5 could completely rescue the defect; however, yeast CAT5 harboring equivalent human pathogenic variants could not. Interestingly, cat5Δ yeast harboring p.Arg57Gln (equivalent to human p.Arg54Gln), p.Arg112Trp (equivalent to p.Arg107Trp), p.Ile69Asn (equivalent to p.Ile66Asn) and combination of p.Lys108Met and p.Leu116Pro (equivalent to the complex allele p.[Thr103Met;Leu111Pro]) partially rescued the growth defects, indicating these variants are hypomorphic alleles. Supplementation with 2,4 dihydroxybenzoic acid (2,4-diHB) rescued the growth defect of both the leaky and severe mutants. Overexpression of COQ8 and 2,4-diHB supplementation synergistically restored oxidative growth and respiratory defect. Overall, we define two distinct disease presentations of COQ7-related disorder with emerging genotype-phenotype correlation and validate the use of the yeast model for functional studies of COQ7 variants.
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Affiliation(s)
- Parith Wongkittichote
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA; Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Maria Laura Duque Lasio
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Martina Magistrati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy
| | - Sheel Pathak
- Division of Pediatric Neurology, Department of Neurology, Washington University School of Medicine, St Louis, MO, USA
| | | | - Daniel Rocha Carvalho
- SARAH Network Rehabilitation Hospitals, Genetic Unit, Brasilia, Federal District, Brazil
| | | | - Matheus Augusto Araújo Castro
- Mendelics Genomic Analyses, Sao Paulo, Brazil; Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo HCFMUSP, São Paulo, SP, Brazil
| | - Claudio M de Gusmao
- Mendelics Genomic Analyses, Sao Paulo, Brazil; Neurogenetics Unit, Hospital das Clínicas da Faculdade de Medicina da Universidade de São Paulo HCFMUSP, São Paulo, SP, Brazil
| | - Tomi L Toler
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA
| | - Emanuele Bellacchio
- Molecular Genetics and Functional Genomics Research Unit, Bambino Gesù Children's Hospital, IRCCS, Rome, Italy
| | - Cristina Dallabona
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parma, Italy.
| | - Marwan Shinawi
- Division of Genetics and Genomic Medicine, Department of Pediatrics, St. Louis Children's Hospital, Washington University School of Medicine, St. Louis, MO, USA.
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68
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Sankhe GD, Raja R, Singh DP, Bheemireddy S, Rana S, Athira PJ, Dixit NM, Saini DK. Sequestration of histidine kinases by non-cognate response regulators establishes a threshold level of stimulation for bacterial two-component signaling. Nat Commun 2023; 14:4483. [PMID: 37491529 PMCID: PMC10368727 DOI: 10.1038/s41467-023-40095-2] [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: 05/05/2020] [Accepted: 07/12/2023] [Indexed: 07/27/2023] Open
Abstract
Bacterial two-component systems (TCSs) consist of a sensor histidine kinase (HK) that perceives a specific signal, and a cognate response regulator (RR) that modulates the expression of target genes. Positive autoregulation improves TCS sensitivity to stimuli, but may trigger disproportionately large responses to weak signals, compromising bacterial fitness. Here, we combine experiments and mathematical modelling to reveal a general design that prevents such disproportionate responses: phosphorylated HKs (HK~Ps) can be sequestered by non-cognate RRs. We study five TCSs of Mycobacterium tuberculosis and find, for all of them, non-cognate RRs that show higher affinity than cognate RRs for HK~Ps. Indeed, in vitro assays show that HK~Ps preferentially bind higher affinity non-cognate RRs and get sequestered. Mathematical modelling indicates that this sequestration would introduce a 'threshold' stimulus strength for eliciting responses, thereby preventing responses to weak signals. Finally, we construct tunable expression systems in Mycobacterium bovis BCG to show that higher affinity non-cognate RRs suppress responses in vivo.
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Affiliation(s)
- Gaurav D Sankhe
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India
| | - Rubesh Raja
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India
| | - Devendra Pratap Singh
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Sneha Bheemireddy
- Molecular Biophysics Unit, Indian Institute of Science, Bengaluru, India
| | - Subinoy Rana
- Materials Research Centre, Indian Institute of Science, Bengaluru, India
| | - P J Athira
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Narendra M Dixit
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Chemical Engineering, Indian Institute of Science, Bengaluru, India.
| | - Deepak Kumar Saini
- Centre for Biosystems Science and Engineering, Indian Institute of Science, Bengaluru, India.
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India.
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69
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Yan J, Li S, Zhang Y, Hao A, Zhao Q. ZetaDesign: an end-to-end deep learning method for protein sequence design and side-chain packing. Brief Bioinform 2023; 24:bbad257. [PMID: 37429578 DOI: 10.1093/bib/bbad257] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 06/05/2023] [Accepted: 06/21/2023] [Indexed: 07/12/2023] Open
Abstract
Computational protein design has been demonstrated to be the most powerful tool in the last few years among protein designing and repacking tasks. In practice, these two tasks are strongly related but often treated separately. Besides, state-of-the-art deep-learning-based methods cannot provide interpretability from an energy perspective, affecting the accuracy of the design. Here we propose a new systematic approach, including both a posterior probability and a joint probability parts, to solve the two essential questions once for all. This approach takes the physicochemical property of amino acids into consideration and uses the joint probability model to ensure the convergence between structure and amino acid type. Our results demonstrated that this method could generate feasible, high-confidence sequences with low-energy side conformations. The designed sequences can fold into target structures with high confidence and maintain relatively stable biochemical properties. The side chain conformation has a significantly lower energy landscape without delegating to a rotamer library or performing the expensive conformational searches. Overall, we propose an end-to-end method that combines the advantages of both deep learning and energy-based methods. The design results of this model demonstrate high efficiency, and precision, as well as a low energy state and good interpretability.
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Affiliation(s)
- Junyu Yan
- State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, China
| | - Shuai Li
- State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, China
| | - Ying Zhang
- The Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Aimin Hao
- State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, China
| | - Qinping Zhao
- State Key Laboratory of Virtual Reality Technology and Systems, Beihang University, Beijing, China
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70
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Jaszczyszyn I, Bielska W, Gawlowski T, Dudzic P, Satława T, Kończak J, Wilman W, Janusz B, Wróbel S, Chomicz D, Galson JD, Leem J, Kelm S, Krawczyk K. Structural modeling of antibody variable regions using deep learning-progress and perspectives on drug discovery. Front Mol Biosci 2023; 10:1214424. [PMID: 37484529 PMCID: PMC10361724 DOI: 10.3389/fmolb.2023.1214424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/12/2023] [Indexed: 07/25/2023] Open
Abstract
AlphaFold2 has hallmarked a generational improvement in protein structure prediction. In particular, advances in antibody structure prediction have provided a highly translatable impact on drug discovery. Though AlphaFold2 laid the groundwork for all proteins, antibody-specific applications require adjustments tailored to these molecules, which has resulted in a handful of deep learning antibody structure predictors. Herein, we review the recent advances in antibody structure prediction and relate them to their role in advancing biologics discovery.
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Affiliation(s)
- Igor Jaszczyszyn
- NaturalAntibody, Kraków, Poland
- Medical University of Warsaw, Warsaw, Poland
| | - Weronika Bielska
- NaturalAntibody, Kraków, Poland
- Medical University of Lodz, Lodz, Poland
| | | | | | | | | | | | | | | | | | | | - Jinwoo Leem
- Alchemab Therapeutics Ltd., London, United Kingdom
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Yovanno RA, Yu A, Wied TJ, Lau AY. Phosphorylation at Ser65 modulates ubiquitin conformational dynamics. Structure 2023; 31:884-890.e2. [PMID: 37267945 PMCID: PMC10330661 DOI: 10.1016/j.str.2023.05.006] [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: 08/10/2022] [Revised: 03/10/2023] [Accepted: 05/08/2023] [Indexed: 06/04/2023]
Abstract
Ubiquitin phosphorylation at Ser65 increases the population of a rare C-terminally retracted (CR) conformation. Transition between the Major and CR ubiquitin conformations is critical for promoting mitochondrial degradation. The mechanisms by which the Major and CR conformations of Ser65-phosphorylated (pSer65) ubiquitin interconvert, however, remain unresolved. Here, we perform all-atom molecular dynamics simulations using the string method with swarms of trajectories to calculate the lowest free-energy path between these two conformers. Our analysis reveals the existence of a Bent intermediate in which the C-terminal residues of the β5 strand shift to resemble the CR conformation, while pSer65 retains contacts resembling the Major conformation. This stable intermediate was reproduced in well-tempered metadynamics calculations but was less stable for a Gln2Ala mutant that disrupts contacts with pSer65. Lastly, dynamical network modeling reveals that the transition from the Major to CR conformations involves a decoupling of residues near pSer65 from the adjacent β1 strand.
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Affiliation(s)
- Remy A Yovanno
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD 21205, USA
| | - Alvin Yu
- Department of Physiology and Biophysics, University of California, Irvine, 825 Health Sciences Road, Irvine, CA 92697, USA
| | - Tyler J Wied
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD 21205, USA
| | - Albert Y Lau
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, 725 N. Wolfe Street, WBSB 706, Baltimore, MD 21205, USA.
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72
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Hameduh T, Mokry M, Miller AD, Heger Z, Haddad Y. Solvent Accessibility Promotes Rotamer Errors during Protein Modeling with Major Side-Chain Prediction Programs. J Chem Inf Model 2023. [PMID: 37410883 PMCID: PMC10369486 DOI: 10.1021/acs.jcim.3c00134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Side-chain rotamer prediction is one of the most critical late stages in protein 3D structure building. Highly advanced and specialized algorithms (e.g., FASPR, RASP, SCWRL4, and SCWRL4v) optimize this process by use of rotamer libraries, combinatorial searches, and scoring functions. We seek to identify the sources of key rotamer errors as a basis for correcting and improving the accuracy of protein modeling going forward. In order to evaluate the aforementioned programs, we process 2496 high-quality single-chained all-atom filtered 30% homology protein 3D structures and use discretized rotamer analysis to compare original with calculated structures. Among 513,024 filtered residue records, increased amino acid residue-dependent rotamer errors─associated in particular with polar and charged amino acid residues (ARG, LYS, and GLN)─clearly correlate with increased amino acid residue solvent accessibility and an increased residue tendency toward the adoption of non-canonical off rotamers which modeling programs struggle to predict accurately. Understanding the impact of solvent accessibility now appears key to improved side-chain prediction accuracies.
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Affiliation(s)
- Tareq Hameduh
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, CZ-613 00 Brno, Czech Republic
| | - Michal Mokry
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, CZ-613 00 Brno, Czech Republic
| | - Andrew D Miller
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, CZ-613 00 Brno, Czech Republic
- Veterinary Research Institute, Hudcova 296/70, CZ-621 00 Brno, Czech Republic
- KP Therapeutics (Europe) s.r.o., Purkyňova 649/127, CZ-612 00 Brno, Czech Republic
| | - Zbynek Heger
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, CZ-613 00 Brno, Czech Republic
| | - Yazan Haddad
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemědělská 1665/1, CZ-613 00 Brno, Czech Republic
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73
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Kratochvil HT, Watkins LC, Mravic M, Thomaston JL, Nicoludis JM, Somberg NH, Liu L, Hong M, Voth GA, DeGrado WF. Transient water wires mediate selective proton transport in designed channel proteins. Nat Chem 2023; 15:1012-1021. [PMID: 37308712 PMCID: PMC10475958 DOI: 10.1038/s41557-023-01210-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/19/2023] [Indexed: 06/14/2023]
Abstract
Selective proton transport through proteins is essential for forming and using proton gradients in cells. Protons are conducted along hydrogen-bonded 'wires' of water molecules and polar side chains, which, somewhat surprisingly, are often interrupted by dry apolar stretches in the conduction pathways, inferred from static protein structures. Here we hypothesize that protons are conducted through such dry spots by forming transient water wires, often highly correlated with the presence of the excess protons in the water wire. To test this hypothesis, we performed molecular dynamics simulations to design transmembrane channels with stable water pockets interspersed by apolar segments capable of forming flickering water wires. The minimalist designed channels conduct protons at rates similar to viral proton channels, and they are at least 106-fold more selective for H+ over Na+. These studies inform the mechanisms of biological proton conduction and the principles for engineering proton-conductive materials.
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Affiliation(s)
- Huong T Kratochvil
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Laura C Watkins
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA
- Kemper Insurance, Chicago, IL, USA
| | - Marco Mravic
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Department of Integrative Structural and Computational Biology Scripps Research Institute, La Jolla, CA, USA
| | - Jessica L Thomaston
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
| | - John M Nicoludis
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA
- Genentech, San Francisco, CA, USA
| | - Noah H Somberg
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | | | - Mei Hong
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Gregory A Voth
- Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, IL, USA.
| | - William F DeGrado
- Department of Pharmaceutical Chemistry, University of California-San Francisco, San Francisco, CA, USA.
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74
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Zhang C. BeEM: fast and faithful conversion of mmCIF format structure files to PDB format. BMC Bioinformatics 2023; 24:260. [PMID: 37340457 DOI: 10.1186/s12859-023-05388-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 06/16/2023] [Indexed: 06/22/2023] Open
Abstract
BACKGROUND Although mmCIF is the current official format for deposition of protein and nucleic acid structures to the protein data bank (PDB) database, the legacy PDB format is still the primary supported format for many structural bioinformatics tools. Therefore, reliable software to convert mmCIF structure files to PDB files is needed. Unfortunately, existing conversion programs fail to correctly convert many mmCIF files, especially those with many atoms and/or long chain identifies. RESULTS This study proposed BeEM, which converts any mmCIF format structure files to PDB format. BeEM conversion faithfully retains all atomic and chain information, including chain IDs with more than 2 characters, which are not supported by any existing mmCIF to PDB converters. The conversion speed of BeEM is at least ten times faster than existing converters such as MAXIT and Phenix. Part of the reason for the speed improvement is the avoidance of conversion between numerical values and text strings. CONCLUSION BeEM is a fast and accurate tool for mmCIF-to-PDB format conversion, which is a common procedure in structural biology. The source code is available under the BSD licence at https://github.com/kad-ecoli/BeEM/ .
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Affiliation(s)
- Chengxin Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, 48109, USA.
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75
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McPartlon M, Xu J. An end-to-end deep learning method for protein side-chain packing and inverse folding. Proc Natl Acad Sci U S A 2023; 120:e2216438120. [PMID: 37253017 PMCID: PMC10266014 DOI: 10.1073/pnas.2216438120] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 04/24/2023] [Indexed: 06/01/2023] Open
Abstract
Protein side-chain packing (PSCP), the task of determining amino acid side-chain conformations given only backbone atom positions, has important applications to protein structure prediction, refinement, and design. Many methods have been proposed to tackle this problem, but their speed or accuracy is still unsatisfactory. To address this, we present AttnPacker, a deep learning (DL) method for directly predicting protein side-chain coordinates. Unlike existing methods, AttnPacker directly incorporates backbone 3D geometry to simultaneously compute all side-chain coordinates without delegating to a discrete rotamer library or performing expensive conformational search and sampling steps. This enables a significant increase in computational efficiency, decreasing inference time by over 100× compared to the DL-based method DLPacker and physics-based RosettaPacker. Tested on the CASP13 and CASP14 native and nonnative protein backbones, AttnPacker computes physically realistic side-chain conformations, reducing steric clashes and improving both rmsd and dihedral accuracy compared to state-of-the-art methods SCWRL4, FASPR, RosettaPacker, and DLPacker. Different from traditional PSCP approaches, AttnPacker can also codesign sequences and side chains, producing designs with subnative Rosetta energy and high in silico consistency.
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Affiliation(s)
- Matthew McPartlon
- Department of Computer Science, Physical Sciences, The University of Chicago, Chicago, IL60637
| | - Jinbo Xu
- Toyota Technical Institute of Chicago, Chicago, IL60637
- MoleculeMind Inc., Beijing100086, China
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76
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Hassenrück F, Farina-Morillas M, Neumann L, Landini F, Blakemore SJ, Rabipour M, Alvarez-Idaboy JR, Pallasch CP, Hallek M, Rebollido-Rios R, Krause G. Functional impact and molecular binding modes of drugs that target the PI3K isoform p110δ. Commun Biol 2023; 6:603. [PMID: 37277510 DOI: 10.1038/s42003-023-04921-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2022] [Accepted: 05/08/2023] [Indexed: 06/07/2023] Open
Abstract
Targeting the PI3K isoform p110δ against B cell malignancies is at the mainstay of PI3K inhibitor (PI3Ki) development. Therefore, we generated isogenic cell lines, which express wild type or mutant p110δ, for assessing the potency, isoform-selectivity and molecular interactions of various PI3Ki chemotypes. The affinity pocket mutation I777M maintains p110δ activity in the presence of idelalisib, as indicated by intracellular AKT phosphorylation, and rescues cell functions such as p110δ-dependent cell viability. Resistance owing to this substitution consistently affects the potency of p110δ-selective in contrast to most multi-targeted PI3Ki, thus distinguishing usually propeller-shaped and typically flat molecules. Accordingly, molecular dynamics simulations indicate that the I777M substitution disturbs conformational flexibility in the specificity or affinity pockets of p110δ that is necessary for binding idelalisib or ZSTK474, but not copanlisib. In summary, cell-based and molecular exploration provide comparative characterization of currently developed PI3Ki and structural insights for future PI3Ki design.
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Affiliation(s)
- Floyd Hassenrück
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Maria Farina-Morillas
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Lars Neumann
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Francesco Landini
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Stuart James Blakemore
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Mina Rabipour
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Juan Raul Alvarez-Idaboy
- Facultad de Química, Departamento de Física y Química Teórica, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Christian P Pallasch
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Michael Hallek
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany
- Center for Molecular Medicine Cologne, Cologne, Germany
| | - Rocio Rebollido-Rios
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany.
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany.
- Center for Molecular Medicine Cologne, Cologne, Germany.
| | - Günter Krause
- University of Cologne, Faculty of Medicine and Cologne University Hospital, Department I of Internal Medicine; Center for Integrated Oncology Aachen, Bonn, Cologne, Düsseldorf, Cologne, Germany.
- CECAD Cologne Cluster of Excellence on Cellular Stress Responses in Aging-Associated Diseases, Cologne, Germany.
- Center for Molecular Medicine Cologne, Cologne, Germany.
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Xiao S, Alshahrani M, Gupta G, Tao P, Verkhivker G. Markov State Models and Perturbation-Based Approaches Reveal Distinct Dynamic Signatures and Hidden Allosteric Pockets in the Emerging SARS-Cov-2 Spike Omicron Variants Complexes with the Host Receptor: The Interplay of Dynamics and Convergent Evolution Modulates Allostery and Functional Mechanisms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.20.541592. [PMID: 37292827 PMCID: PMC10245745 DOI: 10.1101/2023.05.20.541592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The new generation of SARS-CoV-2 Omicron variants displayed a significant growth advantage and the increased viral fitness by acquiring convergent mutations, suggesting that the immune pressure can promote convergent evolution leading to the sudden acceleration of SARS-CoV-2 evolution. In the current study, we combined structural modeling, extensive microsecond MD simulations and Markov state models to characterize conformational landscapes and identify specific dynamic signatures of the SARS-CoV-2 spike complexes with the host receptor ACE2 for the recently emerged highly transmissible XBB.1, XBB.1.5, BQ.1, and BQ.1.1 Omicron variants. Microsecond simulations and Markovian modeling provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the XBB.1.5 subvariant which is contrasted to more dynamic BQ.1 and BQ.1.1 subvariants. Despite considerable structural similarities, Omicron mutations can induce unique dynamic signatures and specific distributions of conformational states. The results suggested that variant-specific changes of conformational mobility in the functional interfacial loops of the spike receptor binding domain can be fine-tuned through cross-talk between convergent mutations thereby providing an evolutionary path for modulation of immune escape. By combining atomistic simulations and Markovian modeling analysis with perturbation-based approaches, we determined important complementary roles of convergent mutation sites as effectors and receivers of allosteric signaling involved in modulating conformational plasticity at the binding interface and regulating allosteric responses. This study also characterized the dynamics-induced evolution of allosteric pockets in the Omicron complexes that revealed hidden allosteric pockets and suggested that convergent mutation sites could control evolution and distribution of allosteric pockets through modulation of conformational plasticity in the flexible adaptable regions. Through integrative computational approaches, this investigation provides a systematic analysis and comparison of the effects of Omicron subvariants on conformational dynamics and allosteric signaling in the complexes with the ACE2 receptor. For Table of Contents Use Only
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78
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Verkhivker G, Alshahrani M, Gupta G. Balancing Functional Tradeoffs between Protein Stability and ACE2 Binding in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic and Energetic Changes. Viruses 2023; 15:1143. [PMID: 37243229 PMCID: PMC10221141 DOI: 10.3390/v15051143] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 04/27/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling a balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; (M.A.); (G.G.)
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79
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Di Rienzo L, Miotto M, Milanetti E, Ruocco G. Computational structural-based GPCR optimization for user-defined ligand: Implications for the development of biosensors. Comput Struct Biotechnol J 2023; 21:3002-3009. [PMID: 37249971 PMCID: PMC10220229 DOI: 10.1016/j.csbj.2023.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/17/2023] [Accepted: 05/04/2023] [Indexed: 05/31/2023] Open
Abstract
Organisms have developed effective mechanisms to sense the external environment. Human-designed biosensors exploit this natural optimization, where different biological machinery have been adapted to detect the presence of user-defined molecules. Specifically, the pheromone pathway in the model organism Saccharomyces cerevisiae represents a suitable candidate as a synthetic signaling system. Indeed, it expresses just one G-Protein Coupled Receptor (GPCR), Ste2, able to recognize pheromone and initiate the expression of pheromone-dependent genes. To date, the standard procedure to engineer this system relies on the substitution of the yeast GPCR with another one and on the modification of the yeast G-protein to bind the inserted receptor. Here, we propose an innovative computational procedure, based on geometrical and chemical optimization of protein binding pockets, to select the amino acid substitutions required to make the native yeast GPCR able to recognize a user-defined ligand. This procedure would allow the yeast to recognize a wide range of ligands, without a-priori knowledge about a GPCR recognizing them or the corresponding G protein. We used Monte Carlo simulations to design on Ste2 a binding pocket able to recognize epinephrine, selected as a test ligand. We validated Ste2 mutants via molecular docking and molecular dynamics. We verified that the amino acid substitutions we identified make Ste2 able to accommodate and remain firmly bound to epinephrine. Our results indicate that we sampled efficiently the huge space of possible mutants, proposing such a strategy as a promising starting point for the development of a new kind of S.cerevisiae-based biosensors.
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Affiliation(s)
- Lorenzo Di Rienzo
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Mattia Miotto
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| | - Edoardo Milanetti
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Giancarlo Ruocco
- Center for Life Nano- & Neuro-Science, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
- Department of Physics, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy
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80
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Verkhivker G, Alshahrani M, Gupta G, Xiao S, Tao P. Probing Conformational Landscapes of Binding and Allostery in the SARS-CoV-2 Omicron Variant Complexes Using Microsecond Atomistic Simulations and Perturbation-Based Profiling Approaches: Hidden Role of Omicron Mutations as Modulators of Allosteric Signaling and Epistatic Relationships. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539337. [PMID: 37205479 PMCID: PMC10187228 DOI: 10.1101/2023.05.03.539337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this study, we systematically examine the conformational dynamics, binding and allosteric communications in the Omicron BA.1, BA.2, BA.3 and BA.4/BA.5 complexes with the ACE2 host receptor using molecular dynamics simulations and perturbation-based network profiling approaches. Microsecond atomistic simulations provided a detailed characterization of the conformational landscapes and revealed the increased thermodynamic stabilization of the BA.2 variant which is contrasted with the BA.4/BA.5 variants inducing a significant mobility of the complexes. Using ensemble-based mutational scanning of binding interactions, we identified binding affinity and structural stability hotspots in the Omicron complexes. Perturbation response scanning and network-based mutational profiling approaches probed the effect of the Omicron variants on allosteric communications. The results of this analysis revealed specific roles of Omicron mutations as "plastic and evolutionary adaptable" modulators of binding and allostery which are coupled to the major regulatory positions through interaction networks. Through perturbation network scanning of allosteric residue potentials in the Omicron variant complexes, which is performed in the background of the original strain, we identified that the key Omicron binding affinity hotspots N501Y and Q498R could mediate allosteric interactions and epistatic couplings. Our results suggested that the synergistic role of these hotspots in controlling stability, binding and allostery can enable for compensatory balance of fitness tradeoffs with conformationally and evolutionary adaptable immune-escape Omicron mutations. Through integrative computational approaches, this study provides a systematic analysis of the effects of Omicron mutations on thermodynamics, binding and allosteric signaling in the complexes with ACE2 receptor. The findings support a mechanism in which Omicron mutations can evolve to balance thermodynamic stability and conformational adaptability in order to ensure proper tradeoff between stability, binding and immune escape.
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81
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Elena-Real CA, Urbanek A, Lund XL, Morató A, Sagar A, Fournet A, Estaña A, Bellande T, Allemand F, Cortés J, Sibille N, Melki R, Bernadó P. Multi-site-specific isotopic labeling accelerates high-resolution structural investigations of pathogenic huntingtin exon-1. Structure 2023:S0969-2126(23)00126-0. [PMID: 37119819 DOI: 10.1016/j.str.2023.04.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/10/2023] [Accepted: 04/04/2023] [Indexed: 05/01/2023]
Abstract
Huntington's disease neurodegeneration occurs when the number of consecutive glutamines in the huntingtin exon-1 (HTTExon1) exceeds a pathological threshold of 35. The sequence homogeneity of HTTExon1 reduces the signal dispersion in NMR spectra, hampering its structural characterization. By simultaneously introducing three isotopically labeled glutamines in a site-specific manner in multiple concatenated samples, 18 glutamines of a pathogenic HTTExon1 with 36 glutamines were unambiguously assigned. Chemical shift analyses indicate the α-helical persistence in the homorepeat and the absence of an emerging toxic conformation around the pathological threshold. Using the same type of samples, the recognition mechanism of Hsc70 molecular chaperone has been investigated, indicating that it binds to the N17 region of HTTExon1, inducing the partial unfolding of the poly-Q. The proposed strategy facilitates high-resolution structural and functional studies in low-complexity regions.
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Affiliation(s)
- Carlos A Elena-Real
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Annika Urbanek
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Xamuel L Lund
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France; Institut Laue Langevin, 38000 Grenoble, France
| | - Anna Morató
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Amin Sagar
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Aurélie Fournet
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Alejandro Estaña
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France; LAAS-CNRS, Université de Toulouse, CNRS, 31400, Toulouse, France
| | - Tracy Bellande
- Institut François Jacob, Molecular Imaging Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) and Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, CEA-Fontenay-aux-Roses Bâtiment 61, 18, route du Panorama, 92265 Fontenay-aux-Rses cedex, France
| | - Frédéric Allemand
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, Université de Toulouse, CNRS, 31400, Toulouse, France
| | - Nathalie Sibille
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France
| | - Ronald Melki
- Institut François Jacob, Molecular Imaging Center (MIRCen), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA) and Laboratory of Neurodegenerative Diseases, Centre National de la Recherche Scientifique (CNRS), Université Paris-Saclay, CEA-Fontenay-aux-Roses Bâtiment 61, 18, route du Panorama, 92265 Fontenay-aux-Rses cedex, France
| | - Pau Bernadó
- Centre de Biologie Structurale (CBS), Université de Montpellier, INSERM, CNRS, 29, rue de Navacelles, 34090 Montpellier, France.
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Ignatov M, Jindal A, Kotelnikov S, Beglov D, Posternak G, Tang X, Maisonneuve P, Poda G, Batey RA, Sicheri F, Whitty A, Tonge PJ, Vajda S, Kozakov D. High Accuracy Prediction of PROTAC Complex Structures. J Am Chem Soc 2023; 145:7123-7135. [PMID: 36961978 PMCID: PMC10240388 DOI: 10.1021/jacs.2c09387] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2023]
Abstract
The design of PROteolysis-TArgeting Chimeras (PROTACs) requires bringing an E3 ligase into proximity with a target protein to modulate the concentration of the latter through its ubiquitination and degradation. Here, we present a method for generating high-accuracy structural models of E3 ligase-PROTAC-target protein ternary complexes. The method is dependent on two computational innovations: adding a "silent" convolution term to an efficient protein-protein docking program to eliminate protein poses that do not have acceptable linker conformations and clustering models of multiple PROTACs that use the same E3 ligase and target the same protein. Results show that the largest consensus clusters always have high predictive accuracy and that the ensemble of models can be used to predict the dissociation rate and cooperativity of the ternary complex that relate to the degrading activity of the PROTAC. The method is demonstrated by applications to known PROTAC structures and a blind test involving PROTACs against BRAF mutant V600E. The results confirm that PROTACs function by stabilizing a favorable interaction between the E3 ligase and the target protein but do not necessarily exploit the most energetically favorable geometry for interaction between the proteins.
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Affiliation(s)
- Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Akhil Jindal
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Acpharis Inc., Holliston, Massachusetts 01746, USA
| | - Ganna Posternak
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Xiaojing Tang
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Pierre Maisonneuve
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
| | - Gennady Poda
- Drug Discovery Program, Ontario Institute for Cancer Research, Toronto, Ontario L4K-M9W, Canada
- Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Robert A. Batey
- Department of Chemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Frank Sicheri
- Center for Molecular, Cell and Systems Biology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario L4K-M9W, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario L4K-M9W, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario L4K-M9W, Canada
| | - Adrian Whitty
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Peter J. Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts 02215 USA
- Department of Chemistry, Boston University, Boston, Massachusetts 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York 11794, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
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83
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Verkhivker G, Alshahrani M, Gupta G. Coarse-Grained Molecular Simulations and Ensemble-Based Mutational Profiling of Protein Stability in the Different Functional Forms of the SARS-CoV-2 Spike Trimers: Balancing Stability and Adaptability in BA.1, BA.2 and BA.2.75 Variants. Int J Mol Sci 2023; 24:ijms24076642. [PMID: 37047615 PMCID: PMC10094791 DOI: 10.3390/ijms24076642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/29/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable among these variants. A systematic mutational scanning of the inter-protomer interfaces in the spike trimers revealed a group of conserved structural stability hotspots that play a key role in the modulation of functional dynamics and are also involved in the inter-protomer couplings through local contacts and interaction networks with the Omicron mutational sites. The results of mutational scanning provided evidence that BA.2.75 trimers are more stable than BA.2 and comparable in stability to the BA.1 variant. Using dynamic network modeling of the S Omicron BA.1, BA.2, and BA.2.75 trimers, we showed that the key network mediators of allosteric interactions are associated with the major stability hotspots that are interconnected along potential communication pathways. The network analysis of the BA.1, BA.2, and BA.2.75 trimers suggested that the increased thermodynamic stability of the BA.2.75 variant may be linked with the organization and modularity of the residue interaction network that allows for allosteric communications between structural stability hotspots and Omicron mutational sites. This study provided a plausible rationale for a mechanism in which Omicron mutations may evolve by targeting vulnerable sites of conformational adaptability to elicit immune escape while maintaining their control on balancing protein stability and functional fitness through robust allosteric communications with the stability hotspots.
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Affiliation(s)
- Gennady Verkhivker
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
| | - Mohammed Alshahrani
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
| | - Grace Gupta
- Keck Center for Science and Engineering, Graduate Program in Computational and Data Sciences, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA
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84
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Soler MA, Minovski N, Rocchia W, Fortuna S. Replica-exchange optimization of antibody fragments. Comput Biol Chem 2023; 103:107819. [PMID: 36657284 DOI: 10.1016/j.compbiolchem.2023.107819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 12/16/2022] [Accepted: 01/13/2023] [Indexed: 01/15/2023]
Abstract
In the framework of the rational design of macromolecules capable of binding to a specific target for biosensing applications, we here further develop an evolutionary protocol designed to optimize the binding affinity of protein binders. In particular we focus on the optimization of the binding portion of small antibody fragments known as nanobodies (or VHH) and choose the hen egg white lysozyme (HEWL) as our target. By implementing a replica exchange scheme for this optimization, we show that an initial hit is not needed and similar solutions can be found by either optimizing an already known anti-HEWL VHH or a randomly selected binder (here a VHH selective towards another macromolecule). While we believe that exhaustive searches of the mutation space are most appropriate when only few key residues have to be optimized, in case a lead binder is not available the proposed evolutionary algorithm should be instead the method of choice.
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Affiliation(s)
- Miguel A Soler
- Italian Institute of Technology (IIT), Via Melen 83, B Block, Genova, Italy; Department of Mathematics, Computer Science and Physics, University of Udine, Via delle Scienze 206, Udine, Italy
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, SI-1001 Ljubljana, Slovenia; Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, Trieste, Italy
| | - Walter Rocchia
- Italian Institute of Technology (IIT), Via Melen 83, B Block, Genova, Italy
| | - Sara Fortuna
- Italian Institute of Technology (IIT), Via Melen 83, B Block, Genova, Italy; Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri 1, Trieste, Italy.
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85
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Esparza-Perusquía M, Langner T, García-Cruz G, Feldbrügge M, Zavala G, Pardo JP, Martínez F, Flores-Herrera O. Deletion of the ATP20 gene in Ustilago maydis produces an unstable dimer of F 1F O-ATP synthase associated with a decrease in mitochondrial ATP synthesis and a high H 2O 2 production. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2023; 1864:148950. [PMID: 36509127 DOI: 10.1016/j.bbabio.2022.148950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 11/07/2022] [Accepted: 12/02/2022] [Indexed: 12/13/2022]
Abstract
The F1FO-ATP synthase uses the energy stored in the electrochemical proton gradient to synthesize ATP. This complex is found in the inner mitochondrial membrane as a monomer and dimer. The dimer shows higher ATPase activity than the monomer and is essential for cristae folding. The monomer-monomer interface is constituted by subunits a, i/j, e, g, and k. The role of the subunit g in a strict respiratory organism is unknown. A gene knockout was generated in Ustilago maydis to study the role of subunit g on mitochondrial metabolism and cristae architecture. Deletion of the ATP20 gene, encoding the g subunit, did not affect cell growth or glucose consumption, but biomass production was lower in the mutant strain (gΔ strain). Ultrastructure observations showed that mitochondrial size and cristae shape were similar in wild-type and gΔ strains. The mitochondrial membrane potential in both strains had a similar magnitude, but oxygen consumption was higher in the WT strain. ATP synthesis was 20 % lower in the gΔ strain. Additionally, the mutant strain expressed the alternative oxidase in the early stages of growth (exponential phase), probably as a response to ROS stress. Dimer from mutant strain was unstable to digitonin solubilization, avoiding its isolation and kinetic characterization. The isolated monomeric state activated by n-dodecyl-β-D-maltopyranoside showed similar kinetic constants to the monomer from the WT strain. A decrease in mitochondrial ATP synthesis and the presence of the AOX during the exponential growth phase suggests that deletion of the g gene induces ROS stress.
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Affiliation(s)
- Mercedes Esparza-Perusquía
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán, 04510 México, D. F., Mexico
| | - Thorsten Langner
- Institute for Microbiology, Cluster of Excellence on Plant Sciences, Department of Biology, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany; The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Giovanni García-Cruz
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán, 04510 México, D. F., Mexico
| | - Michael Feldbrügge
- The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH, United Kingdom
| | - Guadalupe Zavala
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001 Chamilpa, 62210 Cuernavaca, Morelos, Mexico
| | - Juan Pablo Pardo
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán, 04510 México, D. F., Mexico
| | - Federico Martínez
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán, 04510 México, D. F., Mexico
| | - Oscar Flores-Herrera
- Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Apartado Postal 70-159, Coyoacán, 04510 México, D. F., Mexico.
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86
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Shirai T, Nakai A, Ando E, Fujimoto J, Leach S, Arimori T, Higo D, van Eerden FJ, Tulyeu J, Liu YC, Okuzaki D, Murayama MA, Miyata H, Nunomura K, Lin B, Tani A, Kumanogoh A, Ikawa M, Wing JB, Standley DM, Takagi J, Suzuki K. Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex. Sci Immunol 2023; 8:eadc9324. [PMID: 37000855 DOI: 10.1126/sciimmunol.adc9324] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023]
Abstract
Celastrol, a bioactive molecule extracted from the
Tripterygium wilfordii
plant, has been shown to exhibit anti-inflammatory properties. However, its mechanism of action has not been fully elucidated. Here, we show that celastrol suppresses humoral immune responses and autoimmunity by disabling a protein complex consisting of copper metabolism MURR1 domain–containing (COMMD) 3 and COMMD8 (COMMD3/8 complex), a signaling adaptor for chemoattractant receptors. Having demonstrated the involvement of the COMMD3/8 complex in a mouse model of rheumatoid arthritis, we identified celastrol as a compound that covalently bound to and dissociated the COMMD3/8 complex. Celastrol inhibited B cell migration, reduced antibody responses, and blocked arthritis progression, recapitulating deficiency of the COMMD3/8 complex. These effects of celastrol were abolished in mice expressing a celastrol-resistant mutant of the COMMD3/8 complex. These findings establish that celastrol exerts immunosuppressive activity by targeting the COMMD3/8 complex. Our study suggests that the COMMD3/8 complex is a potentially druggable target in autoimmune diseases and points to celastrol as a lead pharmacologic candidate in this capacity.
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Affiliation(s)
- Taiichiro Shirai
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Akiko Nakai
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Immune Response Dynamics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Emiko Ando
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Jun Fujimoto
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Sarah Leach
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Takao Arimori
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Daisuke Higo
- Thermo Fisher Scientific K.K., Yokohama, Kanagawa, Japan
| | - Floris J. van Eerden
- Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Janyerkye Tulyeu
- Laboratory of Human Single Cell Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Yu-Chen Liu
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
| | - Daisuke Okuzaki
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Laboratory of Human Immunology (Single Cell Genomics), WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Masanori A. Murayama
- Department of Animal Models for Human Diseases, Institute of Biomedical Science, Kansai Medical University, Hirakata, Osaka, Japan
| | - Haruhiko Miyata
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - Kazuto Nunomura
- Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, Suita, Osaka, Japan
| | - Bangzhong Lin
- Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, Suita, Osaka, Japan
| | - Akiyoshi Tani
- Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, Suita, Osaka, Japan
| | - Atsushi Kumanogoh
- Department of Respiratory Medicine and Clinical Immunology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Laboratory of Immunopathology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Masahito Ikawa
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
- Department of Experimental Genome Research, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
| | - James B. Wing
- Laboratory of Human Single Cell Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Daron M. Standley
- Laboratory of Systems Immunology, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Department of Genome Informatics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
| | - Junichi Takagi
- Laboratory for Protein Synthesis and Expression, Institute for Protein Research, Osaka University, Suita, Osaka, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Osaka, Japan
| | - Kazuhiro Suzuki
- Laboratory of Immune Response Dynamics, WPI Immunology Frontier Research Center, Osaka University, Suita, Osaka, Japan
- Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
- Department of Immune Response Dynamics, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
- Center for Infectious Disease Education and Research, Osaka University, Suita, Osaka, Japan
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87
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AL Mughram MH, Catalano C, Herrington NB, Safo MK, Kellogg GE. 3D interaction homology: The hydrophobic residues alanine, isoleucine, leucine, proline and valine play different structural roles in soluble and membrane proteins. Front Mol Biosci 2023; 10:1116868. [PMID: 37056722 PMCID: PMC10086146 DOI: 10.3389/fmolb.2023.1116868] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 02/20/2023] [Indexed: 03/30/2023] Open
Abstract
The aliphatic hydrophobic amino acid residues—alanine, isoleucine, leucine, proline and valine—are among the most common found in proteins. Their structural role in proteins is seemingly obvious: engage in hydrophobic interactions to stabilize secondary, and to a lesser extent, tertiary and quaternary structure. However, favorable hydrophobic interactions involving the sidechains of these residue types are generally less significant than the unfavorable set arising from interactions with polar atoms. Importantly, the constellation of interactions between residue sidechains and their environments can be recorded as three-dimensional maps that, in turn, can be clustered. The clustered average map sets compose a library of interaction profiles encoding interaction strengths, interaction types and the optimal 3D position for the interacting partners. This library is backbone angle-dependent and suggests solvent and lipid accessibility for each unique interaction profile. In this work, in addition to analysis of soluble proteins, a large set of membrane proteins that contained optimized artificial lipids were evaluated by parsing the structures into three distinct components: soluble extramembrane domain, lipid facing transmembrane domain, core transmembrane domain. The aliphatic residues were extracted from each of these sets and passed through our calculation protocol. Notable observations include: the roles of aliphatic residues in soluble proteins and in the membrane protein’s soluble domains are nearly identical, although the latter are slightly more solvent accessible; by comparing maps calculated with sidechain-lipid interactions to maps ignoring those interactions, the potential extent of residue-lipid and residue-interactions can be assessed and likely exploited in structure prediction and modeling; amongst these residue types, the levels of lipid engagement show isoleucine as the most engaged, while the other residues are largely interacting with neighboring helical residues.
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Affiliation(s)
- Mohammed H. AL Mughram
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Noah B. Herrington
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Martin K. Safo
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
| | - Glen E. Kellogg
- Department of Medicinal Chemistry and the Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, United States
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, United States
- *Correspondence: Glen E. Kellogg,
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88
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Chakraborty D, Straub JE, Thirumalai D. Energy landscapes of Aβ monomers are sculpted in accordance with Ostwald's rule of stages. SCIENCE ADVANCES 2023; 9:eadd6921. [PMID: 36947617 PMCID: PMC10032606 DOI: 10.1126/sciadv.add6921] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 02/22/2023] [Indexed: 06/18/2023]
Abstract
The transition from a disordered to an assembly-competent monomeric state (N*) in amyloidogenic sequences is a crucial event in the aggregation cascade. Using a well-calibrated model for intrinsically disordered proteins (IDPs), we show that the N* states, which bear considerable resemblance to the polymorphic fibril structures found in experiments, not only appear as excitations in the free energy landscapes of Aβ40 and Aβ42, but also initiate the aggregation cascade. For Aβ42, the transitions to the different N* states are in accord with Ostwald's rule of stages, with the least stable structures forming ahead of thermodynamically favored ones. The Aβ40 and Aβ42 monomer landscapes exhibit different extents of local frustration, which we show have profound implications in dictating subsequent self-assembly. Using kinetic transition networks, we illustrate that the most favored dimerization routes proceed via N* states. We argue that Ostwald's rule also holds for the aggregation of fused in sarcoma and polyglutamine proteins.
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Affiliation(s)
- Debayan Chakraborty
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin TX 78712, USA
| | - John E. Straub
- Department of Chemistry, Boston University, MA 022155, USA
| | - D. Thirumalai
- Department of Chemistry, The University of Texas at Austin, 105 E 24th Street, Stop A5300, Austin TX 78712, USA
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89
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Doran MH, Baker JL, Dahlberg T, Andersson M, Bullitt E. Three structural solutions for bacterial adhesion pilus stability and superelasticity. Structure 2023; 31:529-540.e7. [PMID: 37001523 PMCID: PMC10164138 DOI: 10.1016/j.str.2023.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 01/18/2023] [Accepted: 03/06/2023] [Indexed: 04/22/2023]
Abstract
Bacterial adhesion pili are key virulence factors that mediate host-pathogen interactions in diverse epithelial environments. Deploying a multimodal approach, we probed the structural basis underpinning the biophysical properties of pili originating from enterotoxigenic (ETEC) and uropathogenic bacteria. Using cryo-electron microscopy we solved the structures of three vaccine target pili from ETEC bacteria, CFA/I, CS17, and CS20. Pairing these and previous pilus structures with force spectroscopy and steered molecular dynamics simulations, we find a strong correlation between subunit-subunit interaction energies and the force required for pilus unwinding, irrespective of genetic similarity. Pili integrate three structural solutions for stabilizing their assemblies: layer-to-layer interactions, N-terminal interactions to distant subunits, and extended loop interactions from adjacent subunits. Tuning of these structural solutions alters the biophysical properties of pili and promotes the superelastic behavior that is essential for sustained bacterial attachment.
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Affiliation(s)
- Matthew H Doran
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA
| | - Joseph L Baker
- Department of Chemistry, The College of New Jersey, Ewing, NJ 08628, USA
| | | | - Magnus Andersson
- Department of Physics, Umeå University, Umeå, Sweden; Umeå Centre for Microbial Research (UCMR), Umeå University, Umeå, Sweden
| | - Esther Bullitt
- Department of Physiology & Biophysics, Boston University Chobanian & Avedisian School of Medicine, Boston, MA 02118, USA.
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90
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Xu G, Wang Q, Ma J. OPUS-Mut: Studying the Effect of Protein Mutation through Side-Chain Modeling. J Chem Theory Comput 2023; 19:1629-1640. [PMID: 36813264 PMCID: PMC10018731 DOI: 10.1021/acs.jctc.2c00847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Predicting the effect of protein mutation is crucial in many applications such as protein design, protein evolution, and genetic disease analysis. Structurally, mutation is basically the replacement of the side chain of a particular residue. Therefore, accurate side-chain modeling is useful in studying the effect of mutation. Here, we propose a computational method, namely, OPUS-Mut, which significantly outperforms other backbone-dependent side-chain modeling methods including our previous method OPUS-Rota4. We evaluate OPUS-Mut by four case studies on Myoglobin, p53, HIV-1 protease, and T4 lysozyme. The results show that the predicted structures of side chains of different mutants are consistent well with their experimentally determined results. In addition, when the residues with significant structural shifts upon the mutation are considered, it is found that the extent of the predicted structural shift of these affected residues can be correlated reasonably well with the functional changes of the mutant measured by experiments. OPUS-Mut can also help one to identify the harmful and benign mutations and thus may guide the construction of a protein with relatively low sequence homology but with a similar structure.
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Affiliation(s)
- Gang Xu
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China.,Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201210, China.,Shanghai AI Laboratory, Shanghai 200030, China
| | - Qinghua Wang
- Center for Biomolecular Innovation, Harcam Biomedicines, Shanghai 200131, China
| | - Jianpeng Ma
- Multiscale Research Institute of Complex Systems, Fudan University, Shanghai 200433, China.,Zhangjiang Fudan International Innovation Center, Fudan University, Shanghai 201210, China.,Shanghai AI Laboratory, Shanghai 200030, China
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91
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Structural and Dynamic Differences between Calreticulin Mutants Associated with Essential Thrombocythemia. Biomolecules 2023; 13:biom13030509. [PMID: 36979444 PMCID: PMC10046389 DOI: 10.3390/biom13030509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 02/28/2023] [Accepted: 03/03/2023] [Indexed: 03/12/2023] Open
Abstract
Essential thrombocythemia (ET) is a blood cancer. ET is characterized by an overproduction of platelets that can lead to thrombosis formation. Platelet overproduction occurs in megakaryocytes through a signaling pathway that could involve JAK2, MPL, or CALR proteins. CALR mutations are associated with 25–30% of ET patients; CALR variants must be dimerized to induce ET. We classified these variants into five classes named A to E; classes A and B are the most frequent classes in patients with ET. The dynamic properties of these five classes using structural models of CALR’s C-domain were analyzed using molecular dynamics simulations. Classes A, B, and C are associated with frameshifts in the C-domain. Their dimers can be stable only if a disulfide bond is formed; otherwise, the two monomers repulse each other. Classes D and E cannot be stable as dimers due to the absence of disulfide bonds. Class E and wild-type CALR have similar dynamic properties. These results suggest that the disulfide bond newly formed in classes A, B, and C may be essential for the pathogenicity of these variants. They also underline that class E cannot be directly related to ET but corresponds to human polymorphisms.
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92
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Wang X, Neale C, Kim SK, Goddard WA, Ye L. Intermediate-state-trapped mutants pinpoint G protein-coupled receptor conformational allostery. Nat Commun 2023; 14:1325. [PMID: 36899002 PMCID: PMC10006191 DOI: 10.1038/s41467-023-36971-6] [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: 08/11/2022] [Accepted: 02/16/2023] [Indexed: 03/12/2023] Open
Abstract
Understanding the roles of intermediate states in signaling is pivotal to unraveling the activation processes of G protein-coupled receptors (GPCRs). However, the field is still struggling to define these conformational states with sufficient resolution to study their individual functions. Here, we demonstrate the feasibility of enriching the populations of discrete states via conformation-biased mutants. These mutants adopt distinct distributions among five states that lie along the activation pathway of adenosine A2A receptor (A2AR), a class A GPCR. Our study reveals a structurally conserved cation-π lock between transmembrane helix VI (TM6) and Helix8 that regulates cytoplasmic cavity opening as a "gatekeeper" for G protein penetration. A GPCR activation process based on the well-discerned conformational states is thus proposed, allosterically micro-modulated by the cation-π lock and a previously well-defined ionic interaction between TM3 and TM6. Intermediate-state-trapped mutants will also provide useful information in relation to receptor-G protein signal transduction.
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Affiliation(s)
- Xudong Wang
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA
| | - Chris Neale
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Soo-Kyung Kim
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - William A Goddard
- Materials and Process Simulation Center (139-74), California Institute of Technology, Pasadena, CA, 91125, USA
| | - Libin Ye
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, FL, 33620, USA.
- H. Lee Moffitt Cancer Center & Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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93
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Optical control of PIEZO1 channels. Nat Commun 2023; 14:1269. [PMID: 36882406 PMCID: PMC9992513 DOI: 10.1038/s41467-023-36931-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 02/24/2023] [Indexed: 03/09/2023] Open
Abstract
PIEZO proteins are unusually large, mechanically-activated trimeric ion channels. The central pore features structural similarities with the pore of other trimeric ion channels, including purinergic P2X receptors, for which optical control of channel gating has been previously achieved with photoswitchable azobenzenes. Extension of these chemical optogenetics methods to mechanically-activated ion channels would provide tools for specific manipulation of pore activity alternative to non-specific mechanical stimulations. Here we report a light-gated mouse PIEZO1 channel, in which an azobenzene-based photoswitch covalently tethered to an engineered cysteine, Y2464C, localized at the extracellular apex of the transmembrane helix 38, rapidly triggers channel gating upon 365-nm-light irradiation. We provide evidence that this light-gated channel recapitulates mechanically-activated PIEZO1 functional properties, and show that light-induced molecular motions are similar to those evoked mechanically. These results push the limits of azobenzene-based methods to unusually large ion channels and provide a simple stimulation means to specifically interrogate PIEZO1 function.
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94
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Dong Y, Wang J, Garibsingh RA, Hutchinson K, Shi Y, Eisenberg G, Yu X, Schlessinger A, Grewer C. Conserved allosteric inhibition mechanism in SLC1 transporters. eLife 2023; 12:e83464. [PMID: 36856089 PMCID: PMC10017108 DOI: 10.7554/elife.83464] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 02/27/2023] [Indexed: 03/02/2023] Open
Abstract
Excitatory amino acid transporter 1 (EAAT1) is a glutamate transporter belonging to the SLC1 family of solute carriers. It plays a key role in the regulation of the extracellular glutamate concentration in the mammalian brain. The structure of EAAT1 was determined in complex with UCPH-101, apotent, non-competitive inhibitor of EAAT1. Alanine serine cysteine transporter 2 (ASCT2) is a neutral amino acid transporter, which regulates pools of amino acids such as glutamine between intracellular and extracellular compartments . ASCT2 also belongs to the SLC1 family and shares 58% sequence similarity with EAAT1. However, allosteric modulation of ASCT2 via non-competitive inhibitors is unknown. Here, we explore the UCPH-101 inhibitory mechanisms of EAAT1 and ASCT2 by using rapid kinetic experiments. Our results show that UCPH-101 slows substrate translocation rather than substrate or Na+ binding, confirming a non-competitive inhibitory mechanism, but only partially inhibits wild-type ASCT2. Guided by computational modeling using ligand docking and molecular dynamics simulations, we selected two residues involved in UCPH-101/EAAT1 interaction, which were mutated in ASCT2 (F136Y, I237M, F136Y/I237M) in the corresponding positions. We show that in the F136Y/I237M double-mutant transporter, 100% of the inhibitory effect of UCPH-101 could be restored, and the apparent affinity was increased (Ki = 4.3 μM), much closer to the EAAT1 value of 0.6 μM. Finally, we identify a novel non-competitive ASCT2 inhibitor, through virtual screening and experimental testing against the allosteric site, further supporting its localization. Together, these data indicate that the mechanism of allosteric modulation is conserved between EAAT1 and ASCT2. Due to the difference in binding site residues between ASCT2 and EAAT1, these results raise the possibility that more potent, and potentially selective ASCT2 allosteric inhibitors can be designed .
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Affiliation(s)
- Yang Dong
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
| | - Jiali Wang
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
| | - Rachel-Ann Garibsingh
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Keino Hutchinson
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Yueyue Shi
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
| | - Gilad Eisenberg
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
| | - Xiaozhen Yu
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
| | - Avner Schlessinger
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount SinaiNew YorkUnited States
| | - Christof Grewer
- Department of Chemistry, Binghamton UniversityBinghamtonUnited States
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95
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Shu J, Li J, Wang S, Lin J, Wen L, Ye H, Zhou P. Systematic analysis and comparison of peptide specificity and selectivity between their cognate receptors and noncognate decoys. J Mol Recognit 2023; 36:e3006. [PMID: 36579779 DOI: 10.1002/jmr.3006] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/27/2022] [Indexed: 12/30/2022]
Abstract
Protein-peptide interactions (PpIs) play an important role in cell signaling networks and have been exploited as new and attractive therapeutic targets. The affinity and specificity are two unity-of-opposite aspects of PpIs (and other biomolecular interactions); the former indicates the absolute binding strength between the peptide ligand and its cognate protein receptor in a PpI, while the latter represents the relative recognition selectivity of the peptide ligand for its cognate protein receptor in a PpI over those noncognate decoys that could be potentially encountered by the peptide in cell. Although the PpI binding affinity has been widely investigated over the past decades, the peptide recognition specificity (and selectivity) still remains largely unexplored to date. In this study, we classified PpI specificity into three types: (i) class-I specificity: peptide selectivity for its cognate wild-type protein receptor over the noncognate mutant decoys of this receptor, (ii) class-II specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are homologous with this receptor, and (iii) class-III specificity: peptide selectivity for its cognate protein receptor over other noncognate decoys that are the cognate receptors of other peptides. We performed affinity and selectivity analysis for the three types of PpI specificity and revealed that the PpIs generally exhibit a moderate or modest specificity; peptide selectivity increases in the order: class-I < class-II < class-III. All the three types of PpI specificity were observed to have no statistically significant correlation with peptide length and hydrophobicity, but the class-I and class-II specificities can be influenced considerably by peptide secondary structures; the high specificity is preferentially associated with ordered structure types as compared to undefined structure types. In addition, the mutation distribution (for class-I specificity), sequence conservation (for class-II specificity), and structural similarity (for class-III specificity) seem also to address effects on peptide selectivity.
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Affiliation(s)
- Jianping Shu
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Juelin Li
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Shaozhou Wang
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Jing Lin
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Li Wen
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Haiyang Ye
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
| | - Peng Zhou
- Center for Informational Biology, School of Life Science and Technology, University of Electronic Science and Technology of China (UESTC), Chengdu, China
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96
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Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morató A, Estaña A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortés J, Sinnaeve D, Sibille N, Bernadó P. The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity. Nat Struct Mol Biol 2023; 30:309-320. [PMID: 36864173 DOI: 10.1038/s41594-023-00920-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/05/2023] [Indexed: 03/04/2023]
Abstract
Huntington's disease is a neurodegenerative disorder caused by a CAG expansion in the first exon of the HTT gene, resulting in an extended polyglutamine (poly-Q) tract in huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood due to its intrinsic flexibility and the strong compositional bias. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. Integrative data analysis reveals that the poly-Q tract adopts long α-helical conformations propagated and stabilized by glutamine side chain to backbone hydrogen bonds. We show that α-helical stability is a stronger signature in defining aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. Our observations provide a structural perspective of the pathogenicity of expanded httex1 and pave the way to a deeper understanding of poly-Q-related diseases.
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Affiliation(s)
- Carlos A Elena-Real
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Amin Sagar
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Annika Urbanek
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Matija Popovic
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Anna Morató
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Alejandro Estaña
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Aurélie Fournet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Christine Doucet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Xamuel L Lund
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- Institute of Laue Langevin, Grenoble, France
| | - Zhen-Dan Shi
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Luca Costa
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | | | - Frédéric Allemand
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Rolf E Swenson
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Barcelona, Spain
| | - Alessandro Barducci
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Davy Sinnaeve
- Univ. Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002, Integrative Structural Biology, Lille, France
| | - Nathalie Sibille
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Pau Bernadó
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France.
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97
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GAP positions catalytic H-Ras residue Q61 for GTP hydrolysis in molecular dynamics simulations, complicating chemical rescue of Ras deactivation. Comput Biol Chem 2023; 104:107835. [PMID: 36893567 DOI: 10.1016/j.compbiolchem.2023.107835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 02/01/2023] [Accepted: 02/16/2023] [Indexed: 03/05/2023]
Abstract
Functional interaction of Ras signaling proteins with upstream, negative regulatory GTPase activating proteins (GAPs) represents a crucial step in cellular decision making related to growth and survival. Key components of the catalytic transition state for Ras deactivation by GAP-accelerated hydrolysis of Ras-bound guanosine triphosphate (GTP) are thought to include an arginine residue from the GAP (the arginine finger), a glutamine residue from Ras (Q61), and a water molecule that is likely coordinated by Q61 to engage in nucleophilic attack on GTP. Here, we use in-vitro fluorescence experiments to show that 0.1-100 mM concentrations of free arginine, imidazole, and other small nitrogenous molecule fail to accelerate GTP hydrolysis, even in the presence of the catalytic domain of a mutant GAP lacking its arginine finger (R1276A NF1). This result is surprising given that imidazole can chemically rescue enzyme activity in arginine-to-alanine mutant protein tyrosine kinases (PTKs) that share many active site components with Ras/GAP complexes. Complementary all-atom molecular dynamics (MD) simulations reveal that an arginine finger GAP mutant still functions to enhance Ras Q61-GTP interaction, though less extensively than wild-type GAP. This increased Q61-GTP proximity may promote more frequent fluctuations into configurations that enable GTP hydrolysis as a component of the mechanism by which GAPs accelerate Ras deactivation in the face of arginine finger mutations. The failure of small molecule analogs of arginine to chemically rescue catalytic deactivation of Ras is consistent with the idea that the influence of the GAP goes beyond the simple provision of its arginine finger. However, the failure of chemical rescue in the presence of R1276A NF1 suggests that the GAPs arginine finger is either unsusceptible to rescue due to exquisite positioning or that it is involved in complex multivalent interactions. Therefore, in the context of oncogenic Ras proteins with mutations at codons 12 or 13 that inhibit arginine finger penetration toward GTP, drug-based chemical rescue of GTP hydrolysis may have bifunctional chemical/geometric requirements that are more difficult to satisfy than those that result from arginine-to-alanine mutations in other enzymes for which chemical rescue has been demonstrated.
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98
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Kabir MP, Ouedraogo D, Orozco-Gonzalez Y, Gadda G, Gozem S. Alternative Strategy for Spectral Tuning of Flavin-Binding Fluorescent Proteins. J Phys Chem B 2023; 127:1301-1311. [PMID: 36740810 PMCID: PMC9940217 DOI: 10.1021/acs.jpcb.2c06475] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
iLOV is an engineered flavin-binding fluorescent protein (FbFP) with applications for in vivo cellular imaging. To expand the range of applications of FbFPs for multicolor imaging and FRET-based biosensing, it is desirable to understand how to modify their absorption and emission wavelengths (i.e., through spectral tuning). There is particular interest in developing FbFPs that absorb and emit light at longer wavelengths, which has proven challenging thus far. Existing spectral tuning strategies that do not involve chemical modification of the flavin cofactor have focused on placing positively charged amino acids near flavin's C4a and N5 atoms. Guided by previously reported electrostatic spectral tunning maps (ESTMs) of the flavin cofactor and by quantum mechanical/molecular mechanical (QM/MM) calculations reported in this work, we suggest an alternative strategy: placing a negatively charged amino acid near flavin's N1 atom. We predict that a single-point mutant, iLOV-Q430E, has a slightly red-shifted absorption and fluorescence maximum wavelength relative to iLOV. To validate our theoretical prediction, we experimentally expressed and purified iLOV-Q430E and measured its spectral properties. We found that the Q430E mutation results in a slight change in absorption and a 4-8 nm red shift in the fluorescence relative to iLOV, in good agreement with the computational predictions. Molecular dynamics simulations showed that the carboxylate side chain of the glutamate in iLOV-Q430E points away from the flavin cofactor, which leads to a future expectation that further red shifting may be achieved by bringing the side chain closer to the cofactor.
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99
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Anderson DM, Jayanthi LP, Gosavi S, Meiering EM. Engineering the kinetic stability of a β-trefoil protein by tuning its topological complexity. Front Mol Biosci 2023; 10:1021733. [PMID: 36845544 PMCID: PMC9945329 DOI: 10.3389/fmolb.2023.1021733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 01/02/2023] [Indexed: 02/11/2023] Open
Abstract
Kinetic stability, defined as the rate of protein unfolding, is central to determining the functional lifetime of proteins, both in nature and in wide-ranging medical and biotechnological applications. Further, high kinetic stability is generally correlated with high resistance against chemical and thermal denaturation, as well as proteolytic degradation. Despite its significance, specific mechanisms governing kinetic stability remain largely unknown, and few studies address the rational design of kinetic stability. Here, we describe a method for designing protein kinetic stability that uses protein long-range order, absolute contact order, and simulated free energy barriers of unfolding to quantitatively analyze and predict unfolding kinetics. We analyze two β-trefoil proteins: hisactophilin, a quasi-three-fold symmetric natural protein with moderate stability, and ThreeFoil, a designed three-fold symmetric protein with extremely high kinetic stability. The quantitative analysis identifies marked differences in long-range interactions across the protein hydrophobic cores that partially account for the differences in kinetic stability. Swapping the core interactions of ThreeFoil into hisactophilin increases kinetic stability with close agreement between predicted and experimentally measured unfolding rates. These results demonstrate the predictive power of readily applied measures of protein topology for altering kinetic stability and recommend core engineering as a tractable target for rationally designing kinetic stability that may be widely applicable.
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Affiliation(s)
| | - Lakshmi P. Jayanthi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Shachi Gosavi
- Simons Centre for the Study of Living Machines, National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, India
| | - Elizabeth M. Meiering
- Department of Chemistry, University of Waterloo, Waterloo, ON, Canada,*Correspondence: Elizabeth M. Meiering,
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100
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Abstract
The concentrations of specific macromolecular species can be quantified using diagnostic tools that rely on molecular recognition by nucleic acid aptamers. One such approach involves the formation of osmium tetroxide 2,2'-bipyridine protein adducts, followed by electrochemical detection of analytes that bind specifically to electrode-tethered aptamers. In conjunction with a 27-mer DNA aptamer that binds specifically to exosite II on human alpha thrombin, this technique permits, in theory, a highly sensitive diagnostic tool for the quantification of serum thrombin levels. However, thrombin's aptamer binding site is lined by two tryptophan residues and the conjugation of bulky osmium groups to these residues weakens aptamer binding by an estimated 4 to 12 kcal/mol, undermining detection sensitivity. Therefore, we have rationally modified this DNA aptamer to strengthen its thrombin binding in the presence of conjugated osmium. Specifically, aptamers carrying long hydrophobic thymine derivatives in place of guanine 21 have binding affinities for osmium-conjugated thrombin that are enhanced by 10 to 15 kcal/mol, suggesting that these modified aptamers may be effective in a highly sensitive electrochemical sensor for the quantification of low concentrations of thrombin. Our approach of using molecular simulation to subtly re-engineer a DNA aptamer may be generally applicable for the optimization of other macromolecular binding interfaces.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Loan Huynh
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
| | - Alan Chen
- Department of Chemistry, University at Albany, State University of New York, Albany, NY, USA
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