1
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Rosenberg AA, Yehishalom N, Marx A, Bronstein AM. An amino-domino model described by a cross-peptide-bond Ramachandran plot defines amino acid pairs as local structural units. Proc Natl Acad Sci U S A 2023; 120:e2301064120. [PMID: 37878722 PMCID: PMC10623034 DOI: 10.1073/pnas.2301064120] [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: 01/20/2023] [Accepted: 08/24/2023] [Indexed: 10/27/2023] Open
Abstract
Protein structure, both at the global and local level, dictates function. Proteins fold from chains of amino acids, forming secondary structures, α-helices and β-strands, that, at least for globular proteins, subsequently fold into a three-dimensional structure. Here, we show that a Ramachandran-type plot focusing on the two dihedral angles separated by the peptide bond, and entirely contained within an amino acid pair, defines a local structural unit. We further demonstrate the usefulness of this cross-peptide-bond Ramachandran plot by showing that it captures β-turn conformations in coil regions, that traditional Ramachandran plot outliers fall into occupied regions of our plot, and that thermophilic proteins prefer specific amino acid pair conformations. Further, we demonstrate experimentally that the effect of a point mutation on backbone conformation and protein stability depends on the amino acid pair context, i.e., the identity of the adjacent amino acid, in a manner predictable by our method.
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Affiliation(s)
- Aviv A. Rosenberg
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Nitsan Yehishalom
- Faculty of Biology, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Ailie Marx
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
| | - Alex M. Bronstein
- Department of Computer Science, Technion–Israel Institute of Technology, Haifa32000, Israel
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2
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Robert PA, Akbar R, Frank R, Pavlović M, Widrich M, Snapkov I, Slabodkin A, Chernigovskaya M, Scheffer L, Smorodina E, Rawat P, Mehta BB, Vu MH, Mathisen IF, Prósz A, Abram K, Olar A, Miho E, Haug DTT, Lund-Johansen F, Hochreiter S, Haff IH, Klambauer G, Sandve GK, Greiff V. Unconstrained generation of synthetic antibody-antigen structures to guide machine learning methodology for antibody specificity prediction. NATURE COMPUTATIONAL SCIENCE 2022; 2:845-865. [PMID: 38177393 DOI: 10.1038/s43588-022-00372-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 11/09/2022] [Indexed: 01/06/2024]
Abstract
Machine learning (ML) is a key technology for accurate prediction of antibody-antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction problems and the unavailability of large-scale synthetic datasets to benchmark real-world relevant ML methods and dataset design. Here we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based three-dimensional antibody-antigen-binding structures with ground-truth access to conformational paratope, epitope and affinity. We formalized common immunological antibody-specificity prediction problems as ML tasks and confirmed that for both sequence- and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework has the potential to enable real-world relevant development and benchmarking of ML strategies for biotherapeutics design.
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Affiliation(s)
- Philippe A Robert
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
| | - Rahmad Akbar
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Robert Frank
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Michael Widrich
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | - Igor Snapkov
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Andrei Slabodkin
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Maria Chernigovskaya
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | | | - Eva Smorodina
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Puneet Rawat
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Brij Bhushan Mehta
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway
| | - Mai Ha Vu
- Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway
| | | | - Aurél Prósz
- Danish Cancer Society Research Center, Translational Cancer Genomics, Copenhagen, Denmark
| | - Krzysztof Abram
- The Novo Nordisk Foundation Center for Biosustainability, Autoflow, DTU Biosustain and IT University of Copenhagen, Copenhagen, Denmark
| | - Alex Olar
- Department of Complex Systems in Physics, Eötvös Loránd University, Budapest, Hungary
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
- aiNET GmbH, Basel, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Sepp Hochreiter
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
- Institute of Advanced Research in Artificial Intelligence (IARAI), Vienna, Austria
| | | | - Günter Klambauer
- ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria
| | | | - Victor Greiff
- Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway.
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3
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Akbar R, Robert PA, Pavlović M, Jeliazkov JR, Snapkov I, Slabodkin A, Weber CR, Scheffer L, Miho E, Haff IH, Haug DTT, Lund-Johansen F, Safonova Y, Sandve GK, Greiff V. A compact vocabulary of paratope-epitope interactions enables predictability of antibody-antigen binding. Cell Rep 2021; 34:108856. [PMID: 33730590 DOI: 10.1016/j.celrep.2021.108856] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 11/29/2020] [Accepted: 02/22/2021] [Indexed: 12/16/2022] Open
Abstract
Antibody-antigen binding relies on the specific interaction of amino acids at the paratope-epitope interface. The predictability of antibody-antigen binding is a prerequisite for de novo antibody and (neo-)epitope design. A fundamental premise for the predictability of antibody-antigen binding is the existence of paratope-epitope interaction motifs that are universally shared among antibody-antigen structures. In a dataset of non-redundant antibody-antigen structures, we identify structural interaction motifs, which together compose a commonly shared structure-based vocabulary of paratope-epitope interactions. We show that this vocabulary enables the machine learnability of antibody-antigen binding on the paratope-epitope level using generative machine learning. The vocabulary (1) is compact, less than 104 motifs; (2) distinct from non-immune protein-protein interactions; and (3) mediates specific oligo- and polyreactive interactions between paratope-epitope pairs. Our work leverages combined structure- and sequence-based learning to demonstrate that machine-learning-driven predictive paratope and epitope engineering is feasible.
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Affiliation(s)
- Rahmad Akbar
- Department of Immunology, University of Oslo, Oslo, Norway.
| | | | - Milena Pavlović
- Department of Informatics, University of Oslo, Oslo, Norway; Centre for Bioinformatics, University of Oslo, Norway; K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | | | - Igor Snapkov
- Department of Immunology, University of Oslo, Oslo, Norway
| | | | - Cédric R Weber
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Lonneke Scheffer
- Department of Informatics, University of Oslo, Oslo, Norway; Centre for Bioinformatics, University of Oslo, Norway
| | - Enkelejda Miho
- Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland
| | | | | | | | - Yana Safonova
- Computer Science and Engineering Department, University of California, San Diego, La Jolla, CA, USA
| | - Geir K Sandve
- Department of Informatics, University of Oslo, Oslo, Norway; Centre for Bioinformatics, University of Oslo, Norway; K.G. Jebsen Centre for Coeliac Disease Research, Institute of Clinical Medicine, University of Oslo, Oslo, Norway
| | - Victor Greiff
- Department of Immunology, University of Oslo, Oslo, Norway.
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4
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Tronrud DE, Karplus PA. A complete Fourier-synthesis-based backbone-conformation-dependent library for proteins. Acta Crystallogr D Struct Biol 2021; 77:249-266. [DOI: 10.1107/s2059798320016344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 12/16/2020] [Indexed: 11/10/2022] Open
Abstract
While broadening the applicability of (φ/ψ)-dependent target values for the bond angles in the peptide backbone, sequence/conformation categories with too few residues to analyze via previous methods were encountered. Here, a method of describing a conformation-dependent library (CDL) using two-dimensional Fourier coefficients is reported where the number of coefficients for individual categories is determined via complete cross-validation. Sample sizes are increased further by selective blending of categories with similar patterns of conformational dependence. An additional advantage of the Fourier-synthesis-based CDL is that it uses continuous functions and has no artifactual steps near the edges of populated regions of φ/ψ space. A set of libraries for the seven main-chain bond angles, along with the ω and ζ angles, was created based on a set of Fourier analyses of 48 368 residues selected from high-resolution models in the wwPDB. This new library encompasses both trans- and cis-peptide bonds and outperforms currently used discrete CDLs.
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5
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Riziotis IG, Glykos NM. On the presence of short‐range periodicities in protein structures that are not related to established secondary structure elements. Proteins 2019; 87:966-978. [DOI: 10.1002/prot.25758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 05/21/2019] [Accepted: 06/07/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Ioannis G. Riziotis
- Department of Molecular Biology and GeneticsDemocritus University of Thrace, University campus Alexandroupolis Greece
| | - Nicholas M. Glykos
- Department of Molecular Biology and GeneticsDemocritus University of Thrace, University campus Alexandroupolis Greece
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6
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Malliavin TE, Mucherino A, Lavor C, Liberti L. Systematic Exploration of Protein Conformational Space Using a Distance Geometry Approach. J Chem Inf Model 2019; 59:4486-4503. [PMID: 31442036 DOI: 10.1021/acs.jcim.9b00215] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The optimization approaches classically used during the determination of protein structure encounter various difficulties, especially when the size of the conformational space is large. Indeed, in such a case, algorithmic convergence criteria are more difficult to set up. Moreover, the size of the search space makes it difficult to achieve a complete exploration. The interval branch-and-prune (iBP) approach, based on the reformulation of the distance geometry problem (DGP) provides a theoretical frame for the generation of protein conformations, by systematically sampling the conformational space. When an appropriate subset of interatomic distances is known exactly, this worst-case exponential-time algorithm is provably complete and fixed-parameter tractable. These guarantees, however, immediately disappear as distance measurement errors are introduced. Here we propose an improvement of this approach: threading-augmented interval branch-and-prune (TAiBP), where the combinatorial explosion of the original iBP approach arising from its exponential complexity is alleviated by partitioning the input instances into consecutive peptide fragments and by using self-organizing maps (SOMs) to obtain clusters of similar solutions. A validation of the TAiBP approach is presented here on a set of proteins of various sizes and structures. The calculation inputs are a uniform covalent geometry extracted from force field covalent terms, the backbone dihedral angles with error intervals, and a few long-range distances. For most of the proteins smaller than 50 residues and interval widths of 20°, the TAiBP approach yielded solutions with RMSD values smaller than 3 Å with respect to the initial protein conformation. The efficiency of the TAiBP approach for proteins larger than 50 residues will require the use of nonuniform covalent geometry and may have benefits from the recent development of residue-specific force-fields.
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Affiliation(s)
- Thérèse E Malliavin
- Unité de Bioinformatique Structurale, UMR 3528, CNRS, and Departement de Bioinformatique, Biostatistique et Biologie Intégrative, USR 3756, CNRS , Institut Pasteur , 75015 Paris , France
| | | | - Carlile Lavor
- Applied Math Department , IMECC-University of Campinas , Campinas , SP 13083-970 , Brazil
| | - Leo Liberti
- LIX CNRS, Ecole Polytechnique , Institut Polytechnique de Paris , Route de Saclay , 91128 Palaiseau , France
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7
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Helfrecht BA, Gasparotto P, Giberti F, Ceriotti M. Atomic Motif Recognition in (Bio)Polymers: Benchmarks From the Protein Data Bank. Front Mol Biosci 2019; 6:24. [PMID: 31058166 PMCID: PMC6482324 DOI: 10.3389/fmolb.2019.00024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 03/26/2019] [Indexed: 11/13/2022] Open
Abstract
Rationalizing the structure and structure-property relations for complex materials such as polymers or biomolecules relies heavily on the identification of local atomic motifs, e.g., hydrogen bonds and secondary structure patterns, that are seen as building blocks of more complex supramolecular and mesoscopic structures. Over the past few decades, several automated procedures have been developed to identify these motifs in proteins given the atomic structure. Being based on a very precise understanding of the specific interactions, these heuristic criteria formulate the question in a way that implies the answer, by defining a list of motifs based on those that are known to be naturally occurring. This makes them less likely to identify unexpected phenomena, such as the occurrence of recurrent motifs in disordered segments of proteins, and less suitable to be applied to different polymers whose structure is not driven by hydrogen bonds, or even to polypeptides when appearing in unusual, non-biological conditions. Here we discuss how unsupervised machine learning schemes can be used to recognize patterns based exclusively on the frequency with which different motifs occur, taking high-resolution structures from the Protein Data Bank as benchmarks. We first discuss the application of a density-based motif recognition scheme in combination with traditional representations of protein structure (namely, interatomic distances and backbone dihedrals). Then, we proceed one step further toward an entirely unbiased scheme by using as input a structural representation based on the atomic density and by employing supervised classification to objectively assess the role played by the representation in determining the nature of atomic-scale patterns.
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Affiliation(s)
- Benjamin A Helfrecht
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Piero Gasparotto
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Federico Giberti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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8
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A new clustering and nomenclature for beta turns derived from high-resolution protein structures. PLoS Comput Biol 2019; 15:e1006844. [PMID: 30845191 PMCID: PMC6424458 DOI: 10.1371/journal.pcbi.1006844] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 03/19/2019] [Accepted: 01/31/2019] [Indexed: 11/20/2022] Open
Abstract
Protein loops connect regular secondary structures and contain 4-residue beta turns which represent 63% of the residues in loops. The commonly used classification of beta turns (Type I, I’, II, II’, VIa1, VIa2, VIb, and VIII) was developed in the 1970s and 1980s from analysis of a small number of proteins of average resolution, and represents only two thirds of beta turns observed in proteins (with a generic class Type IV representing the rest). We present a new clustering of beta-turn conformations from a set of 13,030 turns from 1074 ultra-high resolution protein structures (≤1.2 Å). Our clustering is derived from applying the DBSCAN and k-medoids algorithms to this data set with a metric commonly used in directional statistics applied to the set of dihedral angles from the second and third residues of each turn. We define 18 turn types compared to the 8 classical turn types in common use. We propose a new 2-letter nomenclature for all 18 beta-turn types using Ramachandran region names for the two central residues (e.g., ‘A’ and ‘D’ for alpha regions on the left side of the Ramachandran map and ‘a’ and ‘d’ for equivalent regions on the right-hand side; classical Type I turns are ‘AD’ turns and Type I’ turns are ‘ad’). We identify 11 new types of beta turn, 5 of which are sub-types of classical beta-turn types. Up-to-date statistics, probability densities of conformations, and sequence profiles of beta turns in loops were collected and analyzed. A library of turn types, BetaTurnLib18, and cross-platform software, BetaTurnTool18, which identifies turns in an input protein structure, are freely available and redistributable from dunbrack.fccc.edu/betaturn and github.com/sh-maxim/BetaTurn18. Given the ubiquitous nature of beta turns, this comprehensive study updates understanding of beta turns and should also provide useful tools for protein structure determination, refinement, and prediction programs. Folded proteins consist of elements of regular secondary structure, such as alpha helices and beta sheets connected by irregular structures called loops. Loops have a varying length and typically contain U-shaped beta turns which abruptly change the direction of the chain. Beta turns are formed by four sequential amino acid residues and adopt specific conformations which have been classified into eight types since the 1970s. Based on a larger set of very detailed protein structures and thorough statistical data analysis, the previous set of beta-turn types was revised to include 7 existing turn types, 5 subtypes of the existing turns, and 6 new types. Their properties and amino-acid sequence propensities are analyzed. We propose a self-explanatory turn nomenclature, based on the conformations of residues 2 and 3 of the beta turn, that is much easier to remember than the old nomenclature. We developed a library of 18 turn types and software to assign them to an input protein structure. The software and new turn types should advance fundamental understanding of protein structure as well as benefit applications for protein structure prediction, determination, and refinement.
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9
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Gasparotto P, Meißner RH, Ceriotti M. Recognizing Local and Global Structural Motifs at the Atomic Scale. J Chem Theory Comput 2018; 14:486-498. [DOI: 10.1021/acs.jctc.7b00993] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Piero Gasparotto
- Laboratory of Computational
Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Robert Horst Meißner
- Laboratory of Computational
Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michele Ceriotti
- Laboratory of Computational
Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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10
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Kean KM, Porter JJ, Mehl RA, Karplus PA. Structural insights into a thermostable variant of human carbonic anhydrase II. Protein Sci 2017; 27:573-577. [PMID: 29139171 DOI: 10.1002/pro.3347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/08/2017] [Accepted: 11/09/2017] [Indexed: 11/07/2022]
Abstract
Carbonic anhydrase is an enzyme of interest for many biotechnological developments including carbon sequestration. These applications often require harsh conditions, so there is a need for the development of thermostable variants. One of the most thermostable human carbonic anhydrase II (HCAIIts) variants was patented in 2006. Here, we report the ultra-high resolution crystal structure of HCAIIts. The structural changes seen are consistent with each of the six mutations involved acting largely independently and variously resulting in increased H-bonding, improved packing, and reduced side chain entropy loss on folding to yield the increased stability. We further suggest that for four of the mutations, improvements in backbone conformational energetics is also a contributor and that considerations of such conformational propensities of individual amino acids are often overlooked.
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Affiliation(s)
- Kelsey M Kean
- Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, Oregon, 97331
| | - Joseph J Porter
- Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, Oregon, 97331
| | - Ryan A Mehl
- Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, Oregon, 97331
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, 2011 Agriculture and Life Sciences Building, Oregon State University, Corvallis, Oregon, 97331
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11
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Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins. Sci Rep 2017; 7:12433. [PMID: 28970487 PMCID: PMC5624888 DOI: 10.1038/s41598-017-10525-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 08/09/2017] [Indexed: 12/22/2022] Open
Abstract
Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the “downhill” folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide’s conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a “focused chiral mutant library” approach for the unbiased study of amyloid-forming IDPs.
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12
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Yadav P, Shahane G, Gaikwad S. Amaranthus caudatus lectin with polyproline II fold: conformational and functional transitions and molecular dynamics. J Biomol Struct Dyn 2017; 36:2203-2215. [DOI: 10.1080/07391102.2017.1345328] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Priya Yadav
- Academy of Scientific and Innovative Research (AcSIR) NCL campus, Biochemical Sciences Division, CSIR-NCL, Pune, India
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
| | - Ganesh Shahane
- Institute of Bioengineering, Queen Mary University of London, Mile End Road, London, UK
| | - Sushama Gaikwad
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Dr Homi Bhabha Road, Pune 411008, India
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13
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Balaji GA, Nagendra HG, Balaji VN, Rao SN. Experimental conformational energy maps of proteins and peptides. Proteins 2017; 85:979-1001. [PMID: 28168743 DOI: 10.1002/prot.25266] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 01/26/2017] [Accepted: 01/30/2017] [Indexed: 01/26/2023]
Abstract
We have presented an extensive analysis of the peptide backbone dihedral angles in the PDB structures and computed experimental Ramachandran plots for their distributions seen under a various constraints on X-ray resolution, representativeness at different sequence identity percentages, and hydrogen bonding distances. These experimental distributions have been converted into isoenergy contour plots using the approach employed previously by F. M. Pohl. This has led to the identification of energetically favored minima in the Ramachandran (ϕ, ψ) plots in which global minima are predominantly observed either in the right-handed α-helical or the polyproline II regions. Further, we have identified low energy pathways for transitions between various minima in the (ϕ,ψ) plots. We have compared and presented the experimental plots with published theoretical plots obtained from both molecular mechanics and quantum mechanical approaches. In addition, we have developed and employed a root mean square deviation (RMSD) metric for isoenergy contours in various ranges, as a measure (in kcal.mol-1 ) to compare any two plots and determine the extent of correlation and similarity between their isoenergy contours. In general, we observe a greater degree of compatibility with experimental plots for energy maps obtained from molecular mechanics methods compared to most quantum mechanical methods. The experimental energy plots we have investigated could be helpful in refining protein structures obtained from X-ray, NMR, and electron microscopy and in refining force field parameters to enable simulations of peptide and protein structures that have higher degree of consistency with experiments. Proteins 2017; 85:979-1001. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Govardhan A Balaji
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - H G Nagendra
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - Vitukudi N Balaji
- Department of Biotechnology, Sir M Visvesvaraya Institute of Technology, Bangalore, 562157, India
| | - Shashidhar N Rao
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey, 08552
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14
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Adzhubei AA, Anashkina AA, Makarov AA. Left-handed polyproline-II helix revisited: proteins causing proteopathies. J Biomol Struct Dyn 2016; 35:2701-2713. [PMID: 27562438 DOI: 10.1080/07391102.2016.1229220] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Left-handed polyproline-II type helix is a regular conformation of polypeptide chain not only of fibrous, but also of folded and natively unfolded proteins and peptides. It is the only class of regular secondary structure substantially represented in non-fibrous proteins and peptides on a par with right-handed alpha-helix and beta-structure. In this study, we have shown that polyproline-II helix is abundant in several peptides and proteins involved in proteopathies, the amyloid-beta peptides, protein tau and prion protein. Polyproline-II helices form two interaction sites in the amyloid-beta peptides, which are pivotal for pathogenesis of Alzheimer's disease (AD). It also with high probability is the structure of the majority of tau phosphorylation sites, important for tau hyperphosphorylation and formation of neurofibrillary tangles, a hallmark of AD. Polyproline-II helices form large parts of the structure of the folded domain of prion protein. They can undergo conversion to beta-structure as a result of relatively small change of one torsional angle of polypeptide chain. We hypothesize that in prions and amyloids, in general polyproline-II helices can serve as structural elements of the normal structure as well as dormant nuclei of structure conversion, and thus play important role in structure changes leading to the formation of fibrils.
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Affiliation(s)
- Alexei A Adzhubei
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
| | - Anastasia A Anashkina
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
| | - Alexander A Makarov
- a Engelhardt Institute of Molecular Biology, Russian Academy of Sciences , Vavilov St 32, Moscow 119991 , Russia
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15
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Margreitter C, Oostenbrink C. Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting. J Chem Inf Model 2016; 56:1823-34. [PMID: 27559757 PMCID: PMC5039763 DOI: 10.1021/acs.jcim.6b00399] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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Molecular dynamics
simulations depend critically on the accuracy
of the underlying force fields in properly representing biomolecules.
Hence, it is crucial to validate the force-field parameter sets in
this respect. In the context of the GROMOS force field, this is usually
achieved by comparing simulation data to experimental observables
for small molecules. In this study, we develop new amino acid backbone
dihedral angle potential energy parameters based on the widely used
54A7 parameter set by matching to experimental J values
and secondary structure propensity scales. In order to find the most
appropriate backbone parameters, close to 100 000 different
combinations of parameters have been screened. However, since the
sheer number of combinations considered prohibits actual molecular
dynamics simulations for each of them, we instead predicted the values
for every combination using Hamiltonian reweighting. While the original
54A7 parameter set fails to reproduce the experimental data, we are
able to provide parameters that match significantly better. However,
to ensure applicability in the context of larger peptides and full
proteins, further studies have to be undertaken.
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Affiliation(s)
- Christian Margreitter
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- Institute for Molecular Modeling and Simulation, University of Natural Resources and Life Sciences , Muthgasse 18, 1190 Vienna, Austria
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16
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Hollingsworth SA, Lewis MC, Karplus PA. Beyond basins: φ,ψ preferences of a residue depend heavily on the φ,ψ values of its neighbors. Protein Sci 2016; 25:1757-62. [PMID: 27342939 DOI: 10.1002/pro.2973] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/14/2016] [Accepted: 06/16/2016] [Indexed: 11/10/2022]
Abstract
The Ramachandran plot distributions of nonglycine residues from experimentally determined structures are routinely described as grouping into one of six major basins: β, PII , α, αL , ξ and γ'. Recent work describing the most common conformations adopted by pairs of residues in folded proteins [i.e., (φ,ψ)2 -motifs] showed that commonly described major basins are not true single thermodynamic basins, but are composed of distinct subregions that are associated with various conformations of either the preceding or following neighbor residue. Here, as documentation of the extent to which the conformational preferences of a central residue are influenced by the conformations of its two neighbors, we present a set of φ,ψ-plots that are delimited simultaneously by the φ,ψ-angles of its neighboring residues on both sides. The level of influence seen here is typically greater than the influence associated with considering the identities of neighboring residues, implying that the use of this heretofore untapped information can improve the accuracy of structure prediction algorithms and low resolution protein structure refinement.
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Affiliation(s)
- Scott A Hollingsworth
- Department of Molecular Biology and Biochemistry, University of California, Irvine, California, 92697
| | - Matthew C Lewis
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, 97331
| | - P Andrew Karplus
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, 97331
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17
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Nagy G, Oostenbrink C. Dihedral-based segment identification and classification of biopolymers I: proteins. J Chem Inf Model 2014; 54:266-77. [PMID: 24364820 PMCID: PMC3904766 DOI: 10.1021/ci400541d] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2013] [Indexed: 12/29/2022]
Abstract
A new structure classification scheme for biopolymers is introduced, which is solely based on main-chain dihedral angles. It is shown that by dividing a biopolymer into segments containing two central residues, a local classification can be performed. The method is referred to as DISICL, short for Dihedral-based Segment Identification and Classification. Compared to other popular secondary structure classification programs, DISICL is more detailed as it offers 18 distinct structural classes, which may be simplified into a classification in terms of seven more general classes. It was designed with an eye to analyzing subtle structural changes as observed in molecular dynamics simulations of biomolecular systems. Here, the DISICL algorithm is used to classify two databases of protein structures, jointly containing more than 10 million segments. The data is compared to two alternative approaches in terms of the amount of classified residues, average occurrence and length of structural elements, and pair wise matches of the classifications by the different programs. In an accompanying paper (Nagy, G.; Oostenbrink, C. Dihedral-based segment identification and classification of biopolymers II: Polynucleotides. J. Chem. Inf. Model. 2013, DOI: 10.1021/ci400542n), the analysis of polynucleotides is described and applied. Overall, DISICL represents a potentially useful tool to analyze biopolymer structures at a high level of detail.
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Affiliation(s)
- Gabor Nagy
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
| | - Chris Oostenbrink
- University of Natural Resources
and Life Sciences, Institute for Molecular
Modeling and Simulation, Muthgasse 18, 1190 Vienna, Austria
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18
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Zou C, Larisika M, Nagy G, Srajer J, Oostenbrink C, Chen X, Knoll W, Liedberg B, Nowak C. Two-dimensional heterospectral correlation analysis of the redox-induced conformational transition in cytochrome c using surface-enhanced Raman and infrared absorption spectroscopies on a two-layer gold surface. J Phys Chem B 2013; 117:9606-14. [PMID: 23930980 PMCID: PMC3753128 DOI: 10.1021/jp404573q] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
heme protein cytochrome c adsorbed to a two-layer
gold surface modified with a self-assembled monolayer of 2-mercaptoethanol
was analyzed using a two-dimensional (2D) heterospectral correlation
analysis that combined surface-enhanced infrared absorption spectroscopy
(SEIRAS) and surface-enhanced Raman spectroscopy (SERS). Stepwise
increasing electric potentials were applied to alter the redox state
of the protein and to induce conformational changes within the protein
backbone. We demonstrate herein that 2D heterospectral correlation
analysis is a particularly suitable and useful technique for the study
of heme-containing proteins as the two spectroscopies address different
portions of the protein. Thus, by correlating SERS and SEIRAS data
in a 2D plot, we can obtain a deeper understanding of the conformational
changes occurring at the redox center and in the supporting protein
backbone during the electron transfer process. The correlation analyses
are complemented by molecular dynamics calculations to explore the
intramolecular interactions.
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Affiliation(s)
- Changji Zou
- School of Materials Science and Engineering, Nanyang Technological University, Singapore
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