1
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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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2
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Luo S, Wohl S, Zheng W, Yang S. Biophysical and Integrative Characterization of Protein Intrinsic Disorder as a Prime Target for Drug Discovery. Biomolecules 2023; 13:biom13030530. [PMID: 36979465 PMCID: PMC10046839 DOI: 10.3390/biom13030530] [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: 02/10/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Protein intrinsic disorder is increasingly recognized for its biological and disease-driven functions. However, it represents significant challenges for biophysical studies due to its high conformational flexibility. In addressing these challenges, we highlight the complementary and distinct capabilities of a range of experimental and computational methods and further describe integrative strategies available for combining these techniques. Integrative biophysics methods provide valuable insights into the sequence–structure–function relationship of disordered proteins, setting the stage for protein intrinsic disorder to become a promising target for drug discovery. Finally, we briefly summarize recent advances in the development of new small molecule inhibitors targeting the disordered N-terminal domains of three vital transcription factors.
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Affiliation(s)
- Shuqi Luo
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Samuel Wohl
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Wenwei Zheng
- College of Integrative Sciences and Arts, Arizona State University, Mesa, AZ 85212, USA
- Correspondence: (W.Z.); (S.Y.)
| | - Sichun Yang
- Center for Proteomics and Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
- Correspondence: (W.Z.); (S.Y.)
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3
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Cohen T, Halfon M, Carter L, Sharkey B, Jain T, Sivasubramanian A, Schneidman-Duhovny D. Multi-state modeling of antibody-antigen complexes with SAXS profiles and deep-learning models. Methods Enzymol 2022; 678:237-262. [PMID: 36641210 DOI: 10.1016/bs.mie.2022.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Antibodies are an established class of human therapeutics. Epitope characterization is an important part of therapeutic antibody discovery. However, structural characterization of antibody-antigen complexes remains challenging. On the one hand, X-ray crystallography or cryo-electron microscopy provide atomic resolution characterization of the epitope, but the data collection process is typically long and the success rate is low. On the other hand, computational methods for modeling antibody-antigen structures from the individual components frequently suffer from a high false positive rate, rarely resulting in a unique solution. Recent deep learning models for structure prediction are also successful in predicting protein-protein complexes. However, they do not perform well for antibody-antigen complexes. Small Angle X-ray Scattering (SAXS) is a reliable technique for rapid structural characterization of protein samples in solution albeit at low resolution. Here, we present an integrative approach for modeling antigen-antibody complexes using the antibody sequence, antigen structure, and experimentally determined SAXS profiles of the antibody, antigen, and the complex. The method models antibody structures using a novel deep-learning approach, NanoNet. The structures of the antibodies and antigens are represented using multiple 3D conformations to account for compositional and conformational heterogeneity of the protein samples that are used to collect the SAXS data. The complexes are predicted by integrating the SAXS profiles with scoring functions for protein-protein interfaces that are based on statistical potentials and antibody-specific deep-learning models. We validated the method via application to four Fab:EGFR and one Fab:PCSK9 antibody:antigen complexes with experimentally available SAXS datasets. The integrative approach returns accurate predictions (interface RMSD<4Å) in the top five predictions for four out of five complexes (respective interface RMSD values of 1.95, 2.18, 2.66 and 3.87Å), providing support for the utility of such a computational pipeline for epitope characterization during therapeutic antibody discovery.
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Affiliation(s)
- Tomer Cohen
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Matan Halfon
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Lester Carter
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, United States
| | - Beth Sharkey
- High-Throughput Expression, Adimab LLC, Lebanon, NH, United States
| | - Tushar Jain
- Computational Biology, Adimab LLC, Palo Alto, CA, United States
| | | | - Dina Schneidman-Duhovny
- The Rachel and Selim Benin School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel.
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4
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Tersteeg S, Mrozowich T, Henrickson A, Demeler B, Patel TR. Purification and characterization of inorganic pyrophosphatase for in vitro RNA transcription. Biochem Cell Biol 2022; 100:425-436. [PMID: 35926232 PMCID: PMC10311840 DOI: 10.1139/bcb-2022-0118] [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: 11/22/2022] Open
Abstract
Inorganic pyrophosphatase (iPPase) is an enzyme that cleaves pyrophosphate into two phosphate molecules. This enzyme is an essential component of in vitro transcription (IVT) reactions for RNA preparation as it prevents pyrophosphate from precipitating with magnesium, ultimately increasing the rate of the IVT reaction. Large-scale RNA production is often required for biochemical and biophysical characterization studies of RNA, therefore requiring large amounts of IVT reagents. Commercially purchased iPPase is often the most expensive component of any IVT reaction. In this paper, we demonstrate that iPPase can be produced in large quantities and high quality using a reasonably generic laboratory facility and that laboratory-purified iPPase is as effective as commercially available iPPase. Furthermore, using size exclusion chromatography coupled with multi-angle light scattering and dynamic light scattering, analytical ultracentrifugation, and small-angle X-ray scattering, we demonstrate that yeast iPPase can form tetramers and hexamers in solution as well as the enzymatically active dimer. Our work provides a robust protocol for laboratories involved with RNA in vitro transcription to efficiently produce active iPPase, significantly reducing the financial strain of large-scale RNA production.
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Affiliation(s)
- Scott Tersteeg
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA
| | - Trushar R. Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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5
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Gaber A, Pavšič M. Modeling and Structure Determination of Homo-Oligomeric Proteins: An Overview of Challenges and Current Approaches. Int J Mol Sci 2021; 22:9081. [PMID: 34445785 PMCID: PMC8396596 DOI: 10.3390/ijms22169081] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/20/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Protein homo-oligomerization is a very common phenomenon, and approximately half of proteins form homo-oligomeric assemblies composed of identical subunits. The vast majority of such assemblies possess internal symmetry which can be either exploited to help or poses challenges during structure determination. Moreover, aspects of symmetry are critical in the modeling of protein homo-oligomers either by docking or by homology-based approaches. Here, we first provide a brief overview of the nature of protein homo-oligomerization. Next, we describe how the symmetry of homo-oligomers is addressed by crystallographic and non-crystallographic symmetry operations, and how biologically relevant intermolecular interactions can be deciphered from the ordered array of molecules within protein crystals. Additionally, we describe the most important aspects of protein homo-oligomerization in structure determination by NMR. Finally, we give an overview of approaches aimed at modeling homo-oligomers using computational methods that specifically address their internal symmetry and allow the incorporation of other experimental data as spatial restraints to achieve higher model reliability.
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6
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Seffernick JT, Lindert S. Hybrid methods for combined experimental and computational determination of protein structure. J Chem Phys 2020; 153:240901. [PMID: 33380110 PMCID: PMC7773420 DOI: 10.1063/5.0026025] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 11/10/2020] [Indexed: 02/04/2023] Open
Abstract
Knowledge of protein structure is paramount to the understanding of biological function, developing new therapeutics, and making detailed mechanistic hypotheses. Therefore, methods to accurately elucidate three-dimensional structures of proteins are in high demand. While there are a few experimental techniques that can routinely provide high-resolution structures, such as x-ray crystallography, nuclear magnetic resonance (NMR), and cryo-EM, which have been developed to determine the structures of proteins, these techniques each have shortcomings and thus cannot be used in all cases. However, additionally, a large number of experimental techniques that provide some structural information, but not enough to assign atomic positions with high certainty have been developed. These methods offer sparse experimental data, which can also be noisy and inaccurate in some instances. In cases where it is not possible to determine the structure of a protein experimentally, computational structure prediction methods can be used as an alternative. Although computational methods can be performed without any experimental data in a large number of studies, inclusion of sparse experimental data into these prediction methods has yielded significant improvement. In this Perspective, we cover many of the successes of integrative modeling, computational modeling with experimental data, specifically for protein folding, protein-protein docking, and molecular dynamics simulations. We describe methods that incorporate sparse data from cryo-EM, NMR, mass spectrometry, electron paramagnetic resonance, small-angle x-ray scattering, Förster resonance energy transfer, and genetic sequence covariation. Finally, we highlight some of the major challenges in the field as well as possible future directions.
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Affiliation(s)
- Justin T. Seffernick
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
| | - Steffen Lindert
- Department of Chemistry and Biochemistry, Ohio State University, Columbus, Ohio 43210, USA
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7
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Cyclic Peptide Inhibitors of the Tsg101 UEV Protein Interactions Refined through Global Docking and Gaussian Accelerated Molecular Dynamics Simulations. Polymers (Basel) 2020; 12:polym12102235. [PMID: 32998394 PMCID: PMC7650771 DOI: 10.3390/polym12102235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Revised: 09/26/2020] [Accepted: 09/27/2020] [Indexed: 01/08/2023] Open
Abstract
Tsg101 UEV domain proteins are potential targets for virus infection therapy, especially for HIV and Ebola viruses. Peptides are key in curbing virus transmission, and cyclic peptides have a greater survival time than their linear peptides. To date, the accurate prediction of cyclic peptide-protein receptors binding conformations still is challenging because of high peptide flexibility. Here, a useful approach combined the global peptide docking, Gaussian accelerated molecular dynamics (GaMD), two-dimensional (2D) potential of mean force (PMF), normal molecular dynamics (cMD), and solvated interaction energy (SIE) techniques. Then we used this approach to investigate the binding conformations of UEV domain proteins with three cyclic peptides inhibitors. We reported the possible cyclic peptide-UEV domain protein binding conformations via 2D PMF free energy profiles and SIE free energy calculations. The residues Trp145, Tyr147, and Trp148 of the native cyclic peptide (CP1) indeed play essential roles in the cyclic peptides-UEV domain proteins interactions. Our findings might increase the accuracy of cyclic peptide-protein conformational prediction, which may facilitate cyclic peptide inhibitor design. Our approach is expected to further aid in addressing the challenges in cyclic peptide inhibitor design.
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8
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Padhorny D, Porter KA, Ignatov M, Alekseenko A, Beglov D, Kotelnikov S, Ashizawa R, Desta I, Alam N, Sun Z, Brini E, Dill K, Schueler-Furman O, Vajda S, Kozakov D. ClusPro in rounds 38 to 45 of CAPRI: Toward combining template-based methods with free docking. Proteins 2020; 88:1082-1090. [PMID: 32142178 DOI: 10.1002/prot.25887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 02/27/2020] [Accepted: 03/04/2020] [Indexed: 01/01/2023]
Abstract
Targets in the protein docking experiment CAPRI (Critical Assessment of Predicted Interactions) generally present new challenges and contribute to new developments in methodology. In rounds 38 to 45 of CAPRI, most targets could be effectively predicted using template-based methods. However, the server ClusPro required structures rather than sequences as input, and hence we had to generate and dock homology models. The available templates also provided distance restraints that were directly used as input to the server. We show here that such an approach has some advantages. Free docking with template-based restraints using ClusPro reproduced some interfaces suggested by weak or ambiguous templates while not reproducing others, resulting in correct server predicted models. More recently we developed the fully automated ClusPro TBM server that performs template-based modeling and thus can use sequences rather than structures of component proteins as input. The performance of the server, freely available for noncommercial use at https://tbm.cluspro.org, is demonstrated by predicting the protein-protein targets of rounds 38 to 45 of CAPRI.
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Affiliation(s)
- Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Andrey Alekseenko
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.,Institute of Computer Aided Design of the Russian Academy of Sciences, Moscow, Russia
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.,Acpharis Inc., Holliston, Massachusetts, USA
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.,Innopolis University, Innopolis, Russia
| | - Ryota Ashizawa
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Israel Desta
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Nawsad Alam
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Zhuyezi Sun
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Emiliano Brini
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Ken Dill
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.,Department of Physics and Astronomy, Stony Brook University, Stony Brook, New York, USA.,Department of Chemistry, Stony Brook University, Stony Brook, New York, USA
| | - Ora Schueler-Furman
- Department of Microbiology and Molecular Genetics, Institute for Medical Research Israel-Canada, Faculty of Medicine, The Hebrew University, Jerusalem, Israel
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA.,Department of Chemistry, Boston University, Boston, Massachusetts, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
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9
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Alekseenko A, Ignatov M, Jones G, Sabitova M, Kozakov D. Protein-Protein and Protein-Peptide Docking with ClusPro Server. Methods Mol Biol 2020; 2165:157-174. [PMID: 32621224 DOI: 10.1007/978-1-0716-0708-4_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The process of creating a model of the structure formed by a pair of interacting molecules is commonly referred to as docking. Protein docking is one of the most studied topics in computational and structural biology with applications to drug design and beyond. In this chapter, we describe ClusPro, a web server for protein-protein and protein-peptide docking. As an input, the server requires two Protein Data Bank (PDB) files (protein-protein mode) or a PDB file for the protein and a sequence for the ligand (protein-peptide mode). Its output consists of ten models of the resulting structure formed by the two objects upon interaction. The server typically produces results in less than 4 h. The server also provides tools (via "Advanced Options" list) for a user to fine-tune the results using any additional knowledge about the interaction process, e.g., small-angle X-ray scattering (SAXS) profile or distance restraints.
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Affiliation(s)
- Andrey Alekseenko
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.,Institute of Computer Aided Design of the Russian Academy of Sciences, Moscow, Russia
| | - Mikhail Ignatov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA.,Institute of Computer Aided Design of the Russian Academy of Sciences, Moscow, Russia.,Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, USA
| | - George Jones
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA.,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Maria Sabitova
- Department of Mathematics, Queens College and CUNY Graduate Center, Flushing, NY, USA
| | - Dima Kozakov
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA. .,Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA. .,Institute for Advanced Computational Sciences, Stony Brook University, Stony Brook, NY, USA.
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10
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Christoffer C, Terashi G, Shin WH, Aderinwale T, Maddhuri Venkata Subramaniya SR, Peterson L, Verburgt J, Kihara D. Performance and enhancement of the LZerD protein assembly pipeline in CAPRI 38-46. Proteins 2019; 88:948-961. [PMID: 31697428 DOI: 10.1002/prot.25850] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/07/2019] [Accepted: 11/03/2019] [Indexed: 01/17/2023]
Abstract
We report the performance of the protein docking prediction pipeline of our group and the results for Critical Assessment of Prediction of Interactions (CAPRI) rounds 38-46. The pipeline integrates programs developed in our group as well as other existing scoring functions. The core of the pipeline is the LZerD protein-protein docking algorithm. If templates of the target complex are not found in PDB, the first step of our docking prediction pipeline is to run LZerD for a query protein pair. Meanwhile, in the case of human group prediction, we survey the literature to find information that can guide the modeling, such as protein-protein interface information. In addition to any literature information and binding residue prediction, generated docking decoys were selected by a rank aggregation of statistical scoring functions. The top 10 decoys were relaxed by a short molecular dynamics simulation before submission to remove atom clashes and improve side-chain conformations. In these CAPRI rounds, our group, particularly the LZerD server, showed robust performance. On the other hand, there are failed cases where some other groups were successful. To understand weaknesses of our pipeline, we analyzed sources of errors for failed targets. Since we noted that structure refinement is a step that needs improvement, we newly performed a comparative study of several refinement approaches. Finally, we show several examples that illustrate successful and unsuccessful cases by our group.
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Affiliation(s)
| | - Genki Terashi
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Woong-Hee Shin
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Department of Chemistry Education, Sunchon National University, Suncheon, Jeollanam-do, Republic of Korea
| | - Tunde Aderinwale
- Department of Computer Science, Purdue University, West Lafayette, Indiana
| | | | - Lenna Peterson
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Jacob Verburgt
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana
| | - Daisuke Kihara
- Department of Computer Science, Purdue University, West Lafayette, Indiana.,Department of Biological Sciences, Purdue University, West Lafayette, Indiana.,Purdue University Center for Cancer Research, Purdue University, West Lafayette, Indiana.,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio
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11
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Porter KA, Padhorny D, Desta I, Ignatov M, Beglov D, Kotelnikov S, Sun Z, Alekseenko A, Anishchenko I, Cong Q, Ovchinnikov S, Baker D, Vajda S, Kozakov D. Template-based modeling by ClusPro in CASP13 and the potential for using co-evolutionary information in docking. Proteins 2019; 87:1241-1248. [PMID: 31444975 DOI: 10.1002/prot.25808] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 07/21/2019] [Accepted: 07/30/2019] [Indexed: 12/29/2022]
Abstract
As a participant in the joint CASP13-CAPRI46 assessment, the ClusPro server debuted its new template-based modeling functionality. The addition of this feature, called ClusPro TBM, was motivated by the previous CASP-CAPRI assessments and by the proven ability of template-based methods to produce higher-quality models, provided templates are available. In prior assessments, ClusPro submissions consisted of models that were produced via free docking of pre-generated homology models. This method was successful in terms of the number of acceptable predictions across targets; however, analysis of results showed that purely template-based methods produced a substantially higher number of medium-quality models for targets for which there were good templates available. The addition of template-based modeling has expanded ClusPro's ability to produce higher accuracy predictions, primarily for homomeric but also for some heteromeric targets. Here we review the newest additions to the ClusPro web server and discuss examples of CASP-CAPRI targets that continue to drive further development. We also describe ongoing work not yet implemented in the server. This includes the development of methods to improve template-based models and the use of co-evolutionary information for data-assisted free docking.
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Affiliation(s)
- Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Israel Desta
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Mikhail Ignatov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Sergei Kotelnikov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York.,Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Zhuyezi Sun
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts
| | - Andrey Alekseenko
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Ivan Anishchenko
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Qian Cong
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington
| | - Sergey Ovchinnikov
- Center for Systems Biology, Harvard University, Cambridge, Massachusetts
| | - David Baker
- Department of Biochemistry, University of Washington, Seattle, Washington.,Institute for Protein Design, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts.,Department of Chemistry, Boston University, Boston, Massachusetts
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
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12
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Porter KA, Desta I, Kozakov D, Vajda S. What method to use for protein-protein docking? Curr Opin Struct Biol 2019; 55:1-7. [PMID: 30711743 PMCID: PMC6669123 DOI: 10.1016/j.sbi.2018.12.010] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 12/22/2018] [Indexed: 10/27/2022]
Abstract
A number of well-established servers perform 'free' docking of proteins of known structures. In contrast, template-based docking can start from sequences if structures are available for complexes that are homologous to the target. On the basis of the results of the CAPRI-CASP structure prediction experiments, template-based methods yield more accurate predictions if good templates can be found, but generally fail without such templates. However, free global docking, or focused docking around even poor quality template-based models, can still generate acceptable docked structures in these cases. In accordance with the analysis of a benchmark set, free docking of heterodimers yields acceptable or better predictions in the top 10 models for around 40% of structures. However, it is likely that a combination of template-based and free docking methods can perform better for targets that have template structures available. Another way of improving the reliability of predictions is adding experimental information as restraints, an option built into several docking servers.
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Affiliation(s)
- Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Israel Desta
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, NY, USA; Laufer Center for Physical and Quantitative Biology, Stony Brook University, NY, USA.
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Department of Chemistry, Boston University, Boston, MA 02215, USA.
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13
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Wollacott AM, Robinson LN, Ramakrishnan B, Tissire H, Viswanathan K, Shriver Z, Babcock GJ. Structural prediction of antibody-APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data. J Mol Recognit 2019; 32:e2778. [DOI: 10.1002/jmr.2778] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/21/2018] [Accepted: 12/06/2018] [Indexed: 12/29/2022]
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14
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Chen PC, Hennig J. The role of small-angle scattering in structure-based screening applications. Biophys Rev 2018; 10:1295-1310. [PMID: 30306530 PMCID: PMC6233350 DOI: 10.1007/s12551-018-0464-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 09/04/2018] [Indexed: 12/16/2022] Open
Abstract
In many biomolecular interactions, changes in the assembly states and structural conformations of participants can act as a complementary reporter of binding to functional and thermodynamic assays. This structural information is captured by a number of structural biology and biophysical techniques that are viable either as primary screens in small-scale applications or as secondary screens to complement higher throughput methods. In particular, small-angle X-ray scattering (SAXS) reports the average distance distribution between all atoms after orientational averaging. Such information is important when for example investigating conformational changes involved in inhibitory and regulatory mechanisms where binding events do not necessarily cause functional changes. Thus, we summarise here the current and prospective capabilities of SAXS-based screening in the context of other methods that yield structural information. Broad guidelines are also provided to assist readers in preparing screening protocols that are tailored to available X-ray sources.
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Affiliation(s)
- Po-Chia Chen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
| | - Janosch Hennig
- Structural and Computational Biology Unit, European Molecular Biology Laboratory Heidelberg, Meyerhofstrasse 1, 69126, Heidelberg, Germany.
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15
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Ignatov M, Kazennov A, Kozakov D. ClusPro FMFT-SAXS: Ultra-fast Filtering Using Small-Angle X-ray Scattering Data in Protein Docking. J Mol Biol 2018; 430:2249-2255. [DOI: 10.1016/j.jmb.2018.03.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2017] [Revised: 03/08/2018] [Accepted: 03/12/2018] [Indexed: 02/01/2023]
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16
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Nealon JO, Philomina LS, McGuffin LJ. Predictive and Experimental Approaches for Elucidating Protein-Protein Interactions and Quaternary Structures. Int J Mol Sci 2017; 18:E2623. [PMID: 29206185 PMCID: PMC5751226 DOI: 10.3390/ijms18122623] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Revised: 11/29/2017] [Accepted: 11/30/2017] [Indexed: 11/17/2022] Open
Abstract
The elucidation of protein-protein interactions is vital for determining the function and action of quaternary protein structures. Here, we discuss the difficulty and importance of establishing protein quaternary structure and review in vitro and in silico methods for doing so. Determining the interacting partner proteins of predicted protein structures is very time-consuming when using in vitro methods, this can be somewhat alleviated by use of predictive methods. However, developing reliably accurate predictive tools has proved to be difficult. We review the current state of the art in predictive protein interaction software and discuss the problem of scoring and therefore ranking predictions. Current community-based predictive exercises are discussed in relation to the growth of protein interaction prediction as an area within these exercises. We suggest a fusion of experimental and predictive methods that make use of sparse experimental data to determine higher resolution predicted protein interactions as being necessary to drive forward development.
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Affiliation(s)
- John Oliver Nealon
- School of Biological Sciences, University of Reading, Reading RG6 6AS, UK.
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17
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Sønderby P, Rinnan Å, Madsen JJ, Harris P, Bukrinski JT, Peters GHJ. Small-Angle X-ray Scattering Data in Combination with RosettaDock Improves the Docking Energy Landscape. J Chem Inf Model 2017; 57:2463-2475. [DOI: 10.1021/acs.jcim.6b00789] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Pernille Sønderby
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | - Åsmund Rinnan
- Department
of Food Science, Faculty of Science, University of Copenhagen, DK-1958 Frederiksberg C, Denmark
| | - Jesper J. Madsen
- Department
of Chemistry, The University of Chicago, Chicago, Illinois 60637, United States
| | - Pernille Harris
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
| | | | - Günther H. J. Peters
- Department
of Chemistry, Technical University of Denmark, DK-2800 Kongens
Lyngby, Denmark
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18
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Kozakov D, Hall DR, Xia B, Porter KA, Padhorny D, Yueh C, Beglov D, Vajda S. The ClusPro web server for protein-protein docking. Nat Protoc 2017. [PMID: 28079879 DOI: 10.1038/nprot2016169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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Affiliation(s)
- Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
- Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York, USA
| | | | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Kathryn A Porter
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Dzmitry Padhorny
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, New York, USA
| | - Christine Yueh
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
| | - Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, USA
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19
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Abstract
The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.
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20
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Vajda S, Yueh C, Beglov D, Bohnuud T, Mottarella SE, Xia B, Hall DR, Kozakov D. New additions to the ClusPro server motivated by CAPRI. Proteins 2017; 85:435-444. [PMID: 27936493 DOI: 10.1002/prot.25219] [Citation(s) in RCA: 335] [Impact Index Per Article: 47.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2016] [Revised: 11/28/2016] [Accepted: 11/29/2016] [Indexed: 12/12/2022]
Abstract
The heavily used protein-protein docking server ClusPro performs three computational steps as follows: (1) rigid body docking, (2) RMSD based clustering of the 1000 lowest energy structures, and (3) the removal of steric clashes by energy minimization. In response to challenges encountered in recent CAPRI targets, we added three new options to ClusPro. These are (1) accounting for small angle X-ray scattering data in docking; (2) considering pairwise interaction data as restraints; and (3) enabling discrimination between biological and crystallographic dimers. In addition, we have developed an extremely fast docking algorithm based on 5D rotational manifold FFT, and an algorithm for docking flexible peptides that include known sequence motifs. We feel that these developments will further improve the utility of ClusPro. However, CAPRI emphasized several shortcomings of the current server, including the problem of selecting the right energy parameters among the five options provided, and the problem of selecting the best models among the 10 generated for each parameter set. In addition, results convinced us that further development is needed for docking homology models. Finally, we discuss the difficulties we have encountered when attempting to develop a refinement algorithm that would be computationally efficient enough for inclusion in a heavily used server. Proteins 2017; 85:435-444. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sandor Vajda
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Department of Chemistry, Boston University, Boston, Massachusetts, 02215
| | - Christine Yueh
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | - Dmitri Beglov
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | - Tanggis Bohnuud
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215
| | - Scott E Mottarella
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215.,Program in Bioinformatics, Boston University, Boston, Massachusetts, 02215
| | - Bing Xia
- Department of Biomedical Engineering, Boston University, Boston, Massachusetts, 02215
| | | | - Dima Kozakov
- Department of Applied Mathematics and Statistics, Stony Brook University, New York.,Laufer Center for Physical and Quantitative Biology, Stony Brook University, New York
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21
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Schindler C, de Vries S, Sasse A, Zacharias M. SAXS Data Alone can Generate High-Quality Models of Protein-Protein Complexes. Structure 2016; 24:1387-1397. [DOI: 10.1016/j.str.2016.06.007] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/08/2016] [Accepted: 06/08/2016] [Indexed: 11/29/2022]
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22
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Schneidman-Duhovny D, Hammel M, Tainer JA, Sali A. FoXS, FoXSDock and MultiFoXS: Single-state and multi-state structural modeling of proteins and their complexes based on SAXS profiles. Nucleic Acids Res 2016; 44:W424-9. [PMID: 27151198 PMCID: PMC4987932 DOI: 10.1093/nar/gkw389] [Citation(s) in RCA: 349] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Accepted: 04/27/2016] [Indexed: 11/14/2022] Open
Abstract
Small Angle X-ray Scattering (SAXS) is an increasingly common and useful technique for structural characterization of molecules in solution. A SAXS experiment determines the scattering intensity of a molecule as a function of spatial frequency, termed SAXS profile. Here, we describe three web servers for modeling atomic structures based on SAXS profiles. FoXS (Fast X-Ray Scattering) rapidly computes a SAXS profile of a given atomistic model and fits it to an experimental profile. FoXSDock docks two rigid protein structures based on a SAXS profile of their complex. MultiFoXS computes a population-weighted ensemble starting from a single input structure by fitting to a SAXS profile of the protein in solution. We describe the interfaces and capabilities of the servers (salilab.org/foxs), followed by demonstrating their application on Interleukin-33 (IL-33) and its primary receptor ST2.
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Affiliation(s)
- Dina Schneidman-Duhovny
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA
| | - Michal Hammel
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - John A Tainer
- Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA Department of Molecular and Cellular Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA
| | - Andrej Sali
- Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry and California Institute for Quantitative Biosciences (QB3), University of California at San Francisco, CA 94143, USA
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23
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Tian Y, Li L, Han H, Wang W, Wang Y, Ye Z, Guo X. Modification of Spherical Polyelectrolyte Brushes by Layer-by-Layer Self-Assembly as Observed by Small Angle X-ray Scattering. Polymers (Basel) 2016; 8:E145. [PMID: 30979238 PMCID: PMC6432364 DOI: 10.3390/polym8040145] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/14/2016] [Accepted: 04/08/2016] [Indexed: 11/17/2022] Open
Abstract
Multilayer modified spherical polyelectrolyte brushes were prepared through alternate deposition of positively charged poly(allylamine hydrochloride) (PAH) and negatively charged poly-l-aspartic acid (PAsp) onto negatively charged spherical poly(acrylic acid) (PAA) brushes (SPBs) on a poly(styrene) core. The charge reversal determined by the zeta potential indicated the success of layer-by-layer (LBL) deposition. The change of the structure during the construction of multilayer modified SPBs was observed by small-angle X-ray scattering (SAXS). SAXS results indicated that some PAH chains were able to penetrate into the PAA brush for the PAA-PAH double-layer modified SPBs whereas part of the PAH moved towards the outer layer when the PAsp layer was loaded to form a PAA-PAH-PAsp triple-layer system. The multilayer modified SPBs were stable upon changing the pH (5 to 9) and ionic strength (1 to 100 mM). The triple-layer modified SPBs were more tolerated to high pH (even at 11) compared to the double-layer ones. SAXS is proved to be a powerful tool for studying the inner structure of multilayer modified SPBs, which can establish guidelines for the a range of potential applications of multilayer modified SPBs.
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Affiliation(s)
- Yuchuan Tian
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Li Li
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Haoya Han
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Weihua Wang
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Yunwei Wang
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Zhishuang Ye
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
| | - Xuhong Guo
- State-Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai 200237, China.
- Engineering Research Center of Xinjiang Bingtuan of Materials Chemical Engineering, Shihezi University, Xinjiang 832000, China.
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24
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de Vries SJ, Chauvot de Beauchêne I, Schindler CEM, Zacharias M. Cryo-EM Data Are Superior to Contact and Interface Information in Integrative Modeling. Biophys J 2016; 110:785-97. [PMID: 26846888 DOI: 10.1016/j.bpj.2015.12.038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/18/2015] [Accepted: 12/14/2015] [Indexed: 12/29/2022] Open
Abstract
Protein-protein interactions carry out a large variety of essential cellular processes. Cryo-electron microscopy (cryo-EM) is a powerful technique for the modeling of protein-protein interactions at a wide range of resolutions, and recent developments have caused a revolution in the field. At low resolution, cryo-EM maps can drive integrative modeling of the interaction, assembling existing structures into the map. Other experimental techniques can provide information on the interface or on the contacts between the monomers in the complex. This inevitably raises the question regarding which type of data is best suited to drive integrative modeling approaches. Systematic comparison of the prediction accuracy and specificity of the different integrative modeling paradigms is unavailable to date. Here, we compare EM-driven, interface-driven, and contact-driven integrative modeling paradigms. Models were generated for the protein docking benchmark using the ATTRACT docking engine and evaluated using the CAPRI two-star criterion. At 20 Å resolution, EM-driven modeling achieved a success rate of 100%, outperforming the other paradigms even with perfect interface and contact information. Therefore, even very low resolution cryo-EM data is superior in predicting heterodimeric and heterotrimeric protein assemblies. Our study demonstrates that a force field is not necessary, cryo-EM data alone is sufficient to accurately guide the monomers into place. The resulting rigid models successfully identify regions of conformational change, opening up perspectives for targeted flexible remodeling.
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Affiliation(s)
- Sjoerd J de Vries
- Physik-Department T38, Technische Universität München, Garching, Germany.
| | | | - Christina E M Schindler
- Physik-Department T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München, Garching, Germany; Center for Integrated Protein Science Munich (CIPSM) at the Physics Department, Technische Universität München, Garching, Germany
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