Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/M

Keller, Grant L.J.; Weiss, Laura I.; Baker, Brian M.

doi:10.3389/fimmu.2022.887759

Physicochemical Heuristics for Identifying High Fidelity, Near-Native Structural Models of Peptide/M

Journal Article · 01 April 2022 · Front. Immun.

DOI:https://doi.org/10.3389/fimmu.2022.887759· OSTI ID:1871712

Keller, Grant L.J.; Weiss, Laura I.; Baker, Brian M.

Research Organization:: Advanced Photon Source (APS), Argonne National Laboratory (ANL), Argonne, IL (US)

Sponsoring Organization:: DOE - Office Of Science; NIH

OSTI ID:: 1871712

Journal Information:: Front. Immun., Journal Name: Front. Immun. Vol. 13

Country of Publication:: United States

Language:: ENGLISH

References (76)

An immunogenic personal neoantigen vaccine for patients with melanoma Ott, Patrick A.; Hu, Zhuting; Keskin, Derin B. Nature, Vol. 547, Issue 7662 https://doi.org/10.1038/nature22991	journal	July 2017
Improvements to Robotics-Inspired Conformational Sampling in Rosetta Stein, Amelie; Kortemme, Tanja PLoS ONE, Vol. 8, Issue 5 https://doi.org/10.1371/journal.pone.0063090	journal	May 2013
When the Lowest Energy Does Not Induce Native Structures: Parallel Minimization of Multi-Energy Values by Hybridizing Searching Intelligences Lü, Qiang; Xia, Xiao-Yan; Chen, Rong PLoS ONE, Vol. 7, Issue 9 https://doi.org/10.1371/journal.pone.0044967	journal	September 2012
The presentation of SARS-CoV-2 peptides by the common HLA-A∗02:01 molecule Szeto, Christopher; Chatzileontiadou, Demetra S. M.; Nguyen, Andrea T. iScience, Vol. 24, Issue 2 https://doi.org/10.1016/j.isci.2021.102096	journal	February 2021
DeepSeqPan, a novel deep convolutional neural network model for pan-specific class I HLA-peptide binding affinity prediction Liu, Zhonghao; Cui, Yuxin; Xiong, Zheng Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-018-37214-1	journal	January 2019
Tumor neoantigens: building a framework for personalized cancer immunotherapy Gubin, Matthew M.; Artyomov, Maxim N.; Mardis, Elaine R. Journal of Clinical Investigation, Vol. 125, Issue 9 https://doi.org/10.1172/JCI80008	journal	August 2015
Features and development of Coot Emsley, P.; Lohkamp, B.; Scott, W. G. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4 https://doi.org/10.1107/S0907444910007493	journal	March 2010
[20] Processing of X-ray diffraction data collected in oscillation mode Otwinowski, Zbyszek; Minor, Wladek Macromolecular Crystallography Part A, 307-326 https://doi.org/10.1016/S0076-6879(97)76066-X	book	January 1997
General Prediction of Peptide-MHC Binding Modes Using Incremental Docking: A Proof of Concept Antunes, Dinler A.; Devaurs, Didier; Moll, Mark BCB '18: 9th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics, Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics https://doi.org/10.1145/3233547.3233719	conference	August 2018
Targeting of cancer neoantigens with donor-derived T cell receptor repertoires Stronen, E.; Toebes, M.; Kelderman, S. Science, Vol. 352, Issue 6291 https://doi.org/10.1126/science.aaf2288	journal	May 2016
DynaPred: A structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations Antes, I.; Siu, S. W. I.; Lengauer, T. Bioinformatics, Vol. 22, Issue 14 https://doi.org/10.1093/bioinformatics/btl216	journal	July 2006
Deep convolutional neural networks for pan-specific peptide-MHC class I binding prediction Han, Youngmahn; Kim, Dongsup BMC Bioinformatics, Vol. 18, Issue 1 https://doi.org/10.1186/s12859-017-1997-x	journal	December 2017
Personalized RNA mutanome vaccines mobilize poly-specific therapeutic immunity against cancer Sahin, Ugur; Derhovanessian, Evelyna; Miller, Matthias Nature, Vol. 547, Issue 7662 https://doi.org/10.1038/nature23003	journal	July 2017
The Rosetta All-Atom Energy Function for Macromolecular Modeling and Design Alford, Rebecca F.; Leaver-Fay, Andrew; Jeliazkov, Jeliazko R. Journal of Chemical Theory and Computation, Vol. 13, Issue 6 https://doi.org/10.1021/acs.jctc.7b00125	journal	May 2017
Large-Scale Structure-Based Prediction of Stable Peptide Binding to Class I HLAs Using Random Forests Abella, Jayvee R.; Antunes, Dinler A.; Clementi, Cecilia Frontiers in Immunology, Vol. 11 https://doi.org/10.3389/fimmu.2020.01583	journal	July 2020
A Recurrent Mutation in Anaplastic Lymphoma Kinase with Distinct Neoepitope Conformations Toor, Jugmohit S.; Rao, Arjun A.; McShan, Andrew C. Frontiers in Immunology, Vol. 9 https://doi.org/10.3389/fimmu.2018.00099	journal	January 2018
Improving T Cell Receptor On-Target Specificity via Structure-Guided Design Hellman, Lance M.; Foley, Kendra C.; Singh, Nishant K. Molecular Therapy, Vol. 27, Issue 2 https://doi.org/10.1016/j.ymthe.2018.12.010	journal	February 2019
Gapped sequence alignment using artificial neural networks: application to the MHC class I system Andreatta, Massimo; Nielsen, Morten Bioinformatics, Vol. 32, Issue 4 https://doi.org/10.1093/bioinformatics/btv639	journal	October 2015
APE-Gen: A Fast Method for Generating Ensembles of Bound Peptide-MHC Conformations Abella, Jayvee; Antunes, Dinler; Clementi, Cecilia Molecules, Vol. 24, Issue 5 https://doi.org/10.3390/molecules24050881	journal	March 2019
Hepatitis C virus-cross-reactive TCR gene-modified T cells: a model for immunotherapy against diseases with genomic instability Spear, Timothy T.; Riley, Timothy P.; Lyons, Gretchen E. Journal of Leukocyte Biology, Vol. 100, Issue 3 https://doi.org/10.1189/jlb.2A1215-561R	journal	February 2016
MolProbity : all-atom structure validation for macromolecular crystallography Chen, Vincent B.; Arendall, W. Bryan; Headd, Jeffrey J. Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1 https://doi.org/10.1107/S0907444909042073	journal	December 2009
Systematic Comparison of Amber and Rosetta Energy Functions for Protein Structure Evaluation Rubenstein, Aliza B.; Blacklock, Kristin; Nguyen, Hai Journal of Chemical Theory and Computation, Vol. 14, Issue 11 https://doi.org/10.1021/acs.jctc.8b00303	journal	September 2018
Combined Covalent-Electrostatic Model of Hydrogen Bonding Improves Structure Prediction with Rosetta O’Meara, Matthew J.; Leaver-Fay, Andrew; Tyka, Michael D. Journal of Chemical Theory and Computation, Vol. 11, Issue 2 https://doi.org/10.1021/ct500864r	journal	January 2015
Sub-angstrom modeling of complexes between flexible peptides and globular proteins Raveh, Barak; London, Nir; Schueler-Furman, Ora Proteins: Structure, Function, and Bioinformatics https://doi.org/10.1002/prot.22716	journal	January 2010
An unbiased approach to defining bona fide cancer neoepitopes that elicit immune-mediated cancer rejection Brennick, Cory A.; George, Mariam M.; Moussa, Marmar M. Journal of Clinical Investigation, Vol. 131, Issue 3 https://doi.org/10.1172/JCI142823	journal	February 2021
Conversion of a T Cell Antagonist into an Agonist by Repairing a Defect in the TCR/Peptide/MHC Interface Baker, Brian M.; Gagnon, Susan J.; Biddison, William E. Immunity, Vol. 13, Issue 4 https://doi.org/10.1016/S1074-7613(00)00047-9	journal	October 2000
HLA-Arena: A Customizable Environment for the Structural Modeling and Analysis of Peptide-HLA Complexes for Cancer Immunotherapy Antunes, Dinler A.; Abella, Jayvee R.; Hall-Swan, Sarah JCO Clinical Cancer Informatics, Issue 4 https://doi.org/10.1200/CCI.19.00123	journal	September 2020
Structural dissimilarity from self drives neoepitope escape from immune tolerance Devlin, Jason R.; Alonso, Jesus A.; Ayres, Cory M. Nature Chemical Biology, Vol. 16, Issue 11 https://doi.org/10.1038/s41589-020-0610-1	journal	August 2020
Mass spectrometry–driven exploration reveals nuances of neoepitope-driven tumor rejection Ebrahimi-Nik, Hakimeh; Michaux, Justine; Corwin, William L. JCI Insight, Vol. 4, Issue 14 https://doi.org/10.1172/jci.insight.129152	journal	July 2019
Genomic and bioinformatic profiling of mutational neoepitopes reveals new rules to predict anticancer immunogenicity Duan, Fei; Duitama, Jorge; Al Seesi, Sahar The Journal of Experimental Medicine, Vol. 211, Issue 11 https://doi.org/10.1084/jem.20141308	journal	September 2014
Four Small Puzzles That Rosetta Doesn't Solve Das, Rhiju PLoS ONE, Vol. 6, Issue 5 https://doi.org/10.1371/journal.pone.0020044	journal	May 2011
Structure-Based Modeling of SARS-CoV-2 Peptide/HLA-A02 Antigens Nerli, Santrupti; Sgourakis, Nikolaos G. Frontiers in Medical Technology, Vol. 2 https://doi.org/10.3389/fmedt.2020.553478	journal	November 2020
DockTope: a Web-based tool for automated pMHC-I modelling Menegatti Rigo, Maurício; Amaral Antunes, Dinler; Vaz de Freitas, Martiela Scientific Reports, Vol. 5, Issue 1 https://doi.org/10.1038/srep18413	journal	December 2015
Conformational Melding Permits a Conserved Binding Geometry in TCR Recognition of Foreign and Self Molecular Mimics Borbulevych, Oleg Y.; Piepenbrink, Kurt H.; Baker, Brian M. The Journal of Immunology, Vol. 186, Issue 5 https://doi.org/10.4049/jimmunol.1003150	journal	January 2011
Predicting Binding Affinities of Protein Ligands from Three-Dimensional Models: Application to Peptide Binding to Class I Major Histocompatibility Proteins Rognan, Didier; Lauemøller, Sanne Lise; Holm, Arne Journal of Medicinal Chemistry, Vol. 42, Issue 22 https://doi.org/10.1021/jm9910775	journal	November 1999
Highly accurate protein structure prediction with AlphaFold Jumper, John; Evans, Richard; Pritzel, Alexander Nature https://doi.org/10.1038/s41586-021-03819-2	journal	July 2021
Practically Useful: What the R osetta Protein Modeling Suite Can Do for You Kaufmann, Kristian W.; Lemmon, Gordon H.; DeLuca, Samuel L. Biochemistry, Vol. 49, Issue 14 https://doi.org/10.1021/bi902153g	journal	April 2010
Systematic identification of personal tumor-specific neoantigens in chronic lymphocytic leukemia Rajasagi, Mohini; Shukla, Sachet A.; Fritsch, Edward F. Blood, Vol. 124, Issue 3 https://doi.org/10.1182/blood-2014-04-567933	journal	July 2014
A general approach for developing system-specific functions to score protein-ligand docked complexes using support vector inductive logic programming Amini, Ata; Shrimpton, Paul J.; Muggleton, Stephen H. Proteins: Structure, Function, and Bioinformatics, Vol. 69, Issue 4 https://doi.org/10.1002/prot.21782	journal	October 2007
Progress and challenges in high-resolution refinement of protein structure models Misura, Kira M. S.; Baker, David Proteins: Structure, Function, and Bioinformatics, Vol. 59, Issue 1 https://doi.org/10.1002/prot.20376	journal	February 2005
Loss of T Cell Antigen Recognition Arising from Changes in Peptide and Major Histocompatibility Complex Protein Flexibility: IMPLICATIONS FOR VACCINE DESIGN Insaidoo, Francis K.; Borbulevych, Oleg Y.; Hossain, Moushumi Journal of Biological Chemistry, Vol. 286, Issue 46 https://doi.org/10.1074/jbc.M111.283564	journal	September 2011
NetMHCpan-4.0: Improved Peptide–MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data Jurtz, Vanessa; Paul, Sinu; Andreatta, Massimo The Journal of Immunology, Vol. 199, Issue 9 https://doi.org/10.4049/jimmunol.1700893	journal	October 2017
GradDock: rapid simulation and tailored ranking functions for peptide-MHC Class I docking Kyeong, Hyun-Ho; Choi, Yoonjoo; Kim, Hak-Sung Bioinformatics, Vol. 34, Issue 3 https://doi.org/10.1093/bioinformatics/btx589	journal	September 2017
The Role of Neoantigens in Cancer Immunotherapy Zhu, Yueting; Liu, Jiyan Frontiers in Oncology, Vol. 11 https://doi.org/10.3389/fonc.2021.682325	journal	August 2021
Towards automated crystallographic structure refinement with phenix.refine Afonine, Pavel V.; Grosse-Kunstleve, Ralf W.; Echols, Nathaniel Acta Crystallographica Section D Biological Crystallography, Vol. 68, Issue 4 https://doi.org/10.1107/S0907444912001308	journal	March 2012
Structures of MART-126/27–35 Peptide/HLA-A2 Complexes Reveal a Remarkable Disconnect between Antigen Structural Homology and T Cell Recognition Borbulevych, Oleg Y.; Insaidoo, Francis K.; Baxter, Tiffany K. Journal of Molecular Biology, Vol. 372, Issue 5 https://doi.org/10.1016/j.jmb.2007.07.025	journal	October 2007
Structure Based Prediction of Neoantigen Immunogenicity Riley, Timothy P.; Keller, Grant L. J.; Smith, Angela R. Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02047	journal	August 2019
Quantitative prediction of mouse class I MHC peptide binding affinity using support vector machine regression (SVR) models Liu, Wen; Meng, Xiangshan; Xu, Qiqi BMC Bioinformatics, Vol. 7, Issue 1 https://doi.org/10.1186/1471-2105-7-182	journal	March 2006
Structural basis for oligoclonal T cell recognition of a shared p53 cancer neoantigen Wu, Daichao; Gallagher, D. Travis; Gowthaman, Ragul Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-16755-y	journal	June 2020
Structural Prediction of Peptides Bound to MHC Class I Fagerberg, Theres; Cerottini, Jean-Charles; Michielin, Olivier Journal of Molecular Biology, Vol. 356, Issue 2 https://doi.org/10.1016/j.jmb.2005.11.059	journal	February 2006
Accurate prediction of protein structures and interactions using a three-track neural network Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan Science, Vol. 373, Issue 6557 https://doi.org/10.1126/science.abj8754	journal	July 2021
What is a support vector machine? Noble, William S. Nature Biotechnology, Vol. 24, Issue 12 https://doi.org/10.1038/nbt1206-1565	journal	December 2006
Free energy mapping of class I MHC molecules and structural determination of bound peptides Sezerman, Ugur; Vajda, Sandor; Delisi, Charles Protein Science, Vol. 5, Issue 7 https://doi.org/10.1002/pro.5560050706	journal	July 1996
Peptide-Binding Groove Contraction Linked to the Lack of T Cell Response: Using Complex Structure and Energy To Identify Neoantigens Pang, Yuan-Ping; Elsbernd, Laura R.; Block, Matthew S. ImmunoHorizons, Vol. 2, Issue 7 https://doi.org/10.4049/immunohorizons.1800048	journal	August 2018
The Length Distribution and Multiple Specificity of Naturally Presented HLA-I Ligands Gfeller, David; Guillaume, Philippe; Michaux, Justine The Journal of Immunology, Vol. 201, Issue 12 https://doi.org/10.4049/jimmunol.1800914	journal	November 2018
Ranking predicted protein structures with support vector regression Qiu, Jian; Sheffler, Will; Baker, David Proteins: Structure, Function, and Bioinformatics, Vol. 71, Issue 3 https://doi.org/10.1002/prot.21809	journal	November 2007
Molecular dynamics simulations of macromolecular crystals Cerutti, David S.; Case, David A. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 9, Issue 4 https://doi.org/10.1002/wcms.1402	journal	November 2018
Interpreting T-Cell Cross-reactivity through Structure: Implications for TCR-Based Cancer Immunotherapy Antunes, Dinler A.; Rigo, Maurício M.; Freitas, Martiela V. Frontiers in Immunology, Vol. 8 https://doi.org/10.3389/fimmu.2017.01210	journal	October 2017
Modeling the structure of bound peptide ligands to major histocompatibility complex Tong, Joo Chuan; Tan, Tin Wee; Ranganathan, Shoba Protein Science, Vol. 13, Issue 9 https://doi.org/10.1110/ps.04631204	journal	September 2004
PyRosetta: a script-based interface for implementing molecular modeling algorithms using Rosetta Chaudhury, S.; Lyskov, S.; Gray, J. J. Bioinformatics, Vol. 26, Issue 5, p. 689-691 https://doi.org/10.1093/bioinformatics/btq007	journal	January 2010
Machine-learning scoring functions to improve structure-based binding affinity prediction and virtual screening: Machine-learning SFs to improve structure-based binding affinity prediction and virtual screening Ain, Qurrat Ul; Aleksandrova, Antoniya; Roessler, Florian D. Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 5, Issue 6 https://doi.org/10.1002/wcms.1225	journal	August 2015
An in silico—in vitro Pipeline Identifying an HLA-A*02:01+ KRAS G12V+ Spliced Epitope Candidate for a Broad Tumor-Immune Response in Cancer Patients Mishto, Michele; Mansurkhodzhaev, Artem; Ying, Ge Frontiers in Immunology, Vol. 10 https://doi.org/10.3389/fimmu.2019.02572	journal	November 2019
Accurate structure prediction of peptide–MHC complexes for identifying highly immunogenic antigens Park, Min-Sun; Park, Sung Yong; Miller, Keith R. Molecular Immunology, Vol. 56, Issue 1-2 https://doi.org/10.1016/j.molimm.2013.04.011	journal	November 2013
Two Different T Cell Receptors use Different Thermodynamic Strategies to Recognize the Same Peptide/MHC Ligand Davis-Harrison, Rebecca L.; Armstrong, Kathryn M.; Baker, Brian M. Journal of Molecular Biology, Vol. 346, Issue 2 https://doi.org/10.1016/j.jmb.2004.11.063	journal	February 2005
T cell receptor cross-reactivity expanded by dramatic peptide–MHC adaptability Riley, Timothy P.; Hellman, Lance M.; Gee, Marvin H. Nature Chemical Biology, Vol. 14, Issue 10 https://doi.org/10.1038/s41589-018-0130-4	journal	September 2018
Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner Smith, Angela R.; Alonso, Jesus A.; Ayres, Cory M. Proceedings of the National Academy of Sciences, Vol. 118, Issue 4 https://doi.org/10.1073/pnas.2018125118	journal	January 2021
Characterization of CD8 ⁺ T-cell responses to non-anchor-type HLA class I neoantigens with single amino-acid substitutions Shinkawa, Tomoyo; Tokita, Serina; Nakatsugawa, Munehide OncoImmunology, Vol. 10, Issue 1 https://doi.org/10.1080/2162402X.2020.1870062	journal	January 2021
A Molecular Switch Abrogates Glycoprotein 100 (gp100) T-cell Receptor (TCR) Targeting of a Human Melanoma Antigen Bianchi, Valentina; Bulek, Anna; Fuller, Anna Journal of Biological Chemistry, Vol. 291, Issue 17 https://doi.org/10.1074/jbc.M115.707414	journal	April 2016
Knowledge-based structure prediction of MHC class I bound peptides: a study of 23 complexes Schueler-Furman, Ora; Elber, Ron; Margalit, Hanah Folding and Design, Vol. 3, Issue 6 https://doi.org/10.1016/S1359-0278(98)00070-4	journal	November 1998
Predicting MHC-peptide binding affinity by differential boundary tree Feng, Peiyuan; Zeng, Jianyang; Ma, Jianzhu Bioinformatics, Vol. 37, Issue Supplement_1 https://doi.org/10.1093/bioinformatics/btab312	journal	July 2021
Computing the Structure of Bound Peptides Rosenfeld, Rakefet; Zheng, Qiang; Vajda, Sandor Journal of Molecular Biology, Vol. 234, Issue 3 https://doi.org/10.1006/jmbi.1993.1607	journal	December 1993
RCSB Protein Data Bank: powerful new tools for exploring 3D structures of biological macromolecules for basic and applied research and education in fundamental biology, biomedicine, biotechnology, bioengineering and energy sciences Burley, Stephen K.; Bhikadiya, Charmi; Bi, Chunxiao Nucleic Acids Research, Vol. 49, Issue D1 https://doi.org/10.1093/nar/gkaa1038	journal	November 2020
Personal Neoantigen Cancer Vaccines: A Road Not Fully Paved Fritsch, Edward F.; Burkhardt, Ute E.; Hacohen, Nir Cancer Immunology Research, Vol. 8, Issue 12 https://doi.org/10.1158/2326-6066.CIR-20-0526	journal	December 2020
Prediction of neo-epitope immunogenicity reveals TCR recognition determinants and provides insight into immunoediting Schmidt, Julien; Smith, Angela R.; Magnin, Morgane Cell Reports Medicine, Vol. 2, Issue 2 https://doi.org/10.1016/j.xcrm.2021.100194	journal	February 2021
Prediction of Protein Mutational Free Energy: Benchmark and Sampling Improvements Increase Classification Accuracy Frenz, Brandon; Lewis, Steven M.; King, Indigo Frontiers in Bioengineering and Biotechnology, Vol. 8 https://doi.org/10.3389/fbioe.2020.558247	journal	October 2020
Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules Falk, Kirsten; Rötzschke, Olaf; Stevanovié, Stefan Nature, Vol. 351, Issue 6324 https://doi.org/10.1038/351290a0	journal	May 1991

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