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Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. Key aspects of the past 30 years of protein design. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2022; 85:086601. [PMID: 35704983 DOI: 10.1088/1361-6633/ac78ef] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 06/15/2022] [Indexed: 06/15/2023]
Abstract
Proteins are the workhorse of life. They are the building infrastructure of living systems; they are the most efficient molecular machines known, and their enzymatic activity is still unmatched in versatility by any artificial system. Perhaps proteins' most remarkable feature is their modularity. The large amount of information required to specify each protein's function is analogically encoded with an alphabet of just ∼20 letters. The protein folding problem is how to encode all such information in a sequence of 20 letters. In this review, we go through the last 30 years of research to summarize the state of the art and highlight some applications related to fundamental problems of protein evolution.
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Affiliation(s)
- Giulia Magi Meconi
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | - Ivan R Sasselli
- Computational Biophysics Lab, Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramon 182, 20014, Donostia-San Sebastián, Spain
| | | | - Jose N Onuchic
- Center for Theoretical Biological Physics, Department of Physics & Astronomy, Department of Chemistry, Department of Biosciences, Rice University, Houston, TX 77251, United States of America
| | - Ivan Coluzza
- BCMaterials, Basque Center for Materials, Applications and Nanostructures, Bld. Martina Casiano, UPV/EHU Science Park, Barrio Sarriena s/n, 48940 Leioa, Spain
- Basque Foundation for Science, Ikerbasque, 48009, Bilbao, Spain
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2
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Abstract
Allosteric transition, defined as conformational changes induced by ligand binding, is one of the fundamental properties of proteins. Allostery has been observed and characterized in many proteins, and has been recently utilized to control protein function via regulation of protein activity. Here, we review the physical and evolutionary origin of protein allostery, as well as its importance to protein regulation, drug discovery, and biological processes in living systems. We describe recently developed approaches to identify allosteric pathways, connected sets of pairwise interactions that are responsible for propagation of conformational change from the ligand-binding site to a distal functional site. We then present experimental and computational protein engineering approaches for control of protein function by modulation of allosteric sites. As an example of application of these approaches, we describe a synergistic computational and experimental approach to rescue the cystic-fibrosis-associated protein cystic fibrosis transmembrane conductance regulator, which upon deletion of a single residue misfolds and causes disease. This example demonstrates the power of allosteric manipulation in proteins to both elucidate mechanisms of molecular function and to develop therapeutic strategies that rescue those functions. Allosteric control of proteins provides a tool to shine a light on the complex cascades of cellular processes and facilitate unprecedented interrogation of biological systems.
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Affiliation(s)
- Nikolay V Dokholyan
- Department of Biochemistry and Biophysics, University of North Carolina , Chapel Hill, North Carolina 27599, United States
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3
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Ferreira DC, van der Linden MG, de Oliveira LC, Onuchic JN, de Araújo AFP. Information and redundancy in the burial folding code of globular proteins within a wide range of shapes and sizes. Proteins 2016; 84:515-31. [PMID: 26815167 DOI: 10.1002/prot.24998] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Revised: 12/28/2015] [Accepted: 01/19/2016] [Indexed: 11/09/2022]
Abstract
Recent ab initio folding simulations for a limited number of small proteins have corroborated a previous suggestion that atomic burial information obtainable from sequence could be sufficient for tertiary structure determination when combined to sequence-independent geometrical constraints. Here, we use simulations parameterized by native burials to investigate the required amount of information in a diverse set of globular proteins comprising different structural classes and a wide size range. Burial information is provided by a potential term pushing each atom towards one among a small number L of equiprobable concentric layers. An upper bound for the required information is provided by the minimal number of layers L(min) still compatible with correct folding behavior. We obtain L(min) between 3 and 5 for seven small to medium proteins with 50 ≤ Nr ≤ 110 residues while for a larger protein with Nr = 141 we find that L ≥ 6 is required to maintain native stability. We additionally estimate the usable redundancy for a given L ≥ L(min) from the burial entropy associated to the largest folding-compatible fraction of "superfluous" atoms, for which the burial term can be turned off or target layers can be chosen randomly. The estimated redundancy for small proteins with L = 4 is close to 0.8. Our results are consistent with the above-average quality of burial predictions used in previous simulations and indicate that the fraction of approachable proteins could increase significantly with even a mild, plausible, improvement on sequence-dependent burial prediction or on sequence-independent constraints that augment the detectable redundancy during simulations.
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Affiliation(s)
- Diogo C Ferreira
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Marx G van der Linden
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
| | - Leandro C de Oliveira
- Departamento de Física, IBILCE, Universidade Estadual Paulista - UNESP, São José do Rio Preto, SP, 15054-000, Brazil
| | - José N Onuchic
- Center for Theoretical Biological Physics and Departments of Physics and Astronomy, Chemistry and Biosciences Rice University, 6100 Main Street, Houston, Texas, 77005
| | - Antônio F Pereira de Araújo
- Laboratório de Biofísica Teórica e Computacional, Departamento de Biologia Celular, Universidade de Brasília, Brasília, DF, 70910-900, Brazil
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Proctor EA, Ding F, Dokholyan NV. Discrete molecular dynamics. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.4] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Elizabeth A. Proctor
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Feng Ding
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Nikolay V. Dokholyan
- Department of Biochemistry and Biophysics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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Randić M, Zupan J, Balaban AT, Vikić-Topić D, Plavšić D. Graphical Representation of Proteins. Chem Rev 2010; 111:790-862. [PMID: 20939561 DOI: 10.1021/cr800198j] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Milan Randić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Jure Zupan
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Alexandru T. Balaban
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Dražen Vikić-Topić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
| | - Dejan Plavšić
- National Institute of Chemistry, P.O. Box 3430, 1001 Ljubljana, Slovenia; NMR Center, Ruđer Bošković Institute, P.O. Box 180, HR-10002 Zagreb, Croatia; and Texas A&M University at Galveston, Galveston, Texas 77553
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A sequence-compatible amount of native burial information is sufficient for determining the structure of small globular proteins. Proc Natl Acad Sci U S A 2009; 106:19001-4. [PMID: 19858496 DOI: 10.1073/pnas.0910851106] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Protein tertiary structures are known to be encoded in amino acid sequences, but the problem of structure prediction from sequence continues to be a challenge. With this question in mind, recent simulations have shown that atomic burials, as expressed by atom distances to the molecular geometrical center, are sufficiently informative for determining native conformations of small globular proteins. Here we use a simple computational experiment to estimate the amount of this required burial information and find it to be surprisingly small, actually comparable with the stringent limit imposed by sequence statistics. Atomic burials appear to satisfy, therefore, minimal requirements for a putative dominating property in the folding code because they provide an amount of information sufficiently large for structural determination but, at the same time, sufficiently small to be encodable in sequences. In a simple analogy with human communication, atomic burials could correspond to the actual "language" encoded in the amino acid "script" from which the complexity of native conformations is recovered during the folding process.
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Lai Z, Su J, Chen W, Wang C. Uncovering the properties of energy-weighted conformation space networks with a hydrophobic-hydrophilic model. Int J Mol Sci 2009; 10:1808-1823. [PMID: 19468340 PMCID: PMC2680648 DOI: 10.3390/ijms10041808] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2009] [Revised: 03/30/2009] [Accepted: 04/07/2009] [Indexed: 11/16/2022] Open
Abstract
The conformation spaces generated by short hydrophobic-hydrophilic (HP) lattice chains are mapped to conformation space networks (CSNs). The vertices (nodes) of the network are the conformations and the links are the transitions between them. It has been found that these networks have "small-world" properties without considering the interaction energy of the monomers in the chain, i. e. the hydrophobic or hydrophilic amino acids inside the chain. When the weight based on the interaction energy of the monomers in the chain is added to the CSNs, it is found that the weighted networks show the "scale-free" characteristic. In addition, it reveals that there is a connection between the scale-free property of the weighted CSN and the folding dynamics of the chain by investigating the relationship between the scale-free structure of the weighted CSN and the noted parameter Z score. Moreover, the modular (community) structure of weighted CSNs is also studied. These results are helpful to understand the topological properties of the CSN and the underlying free-energy landscapes.
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Affiliation(s)
- Zaizhi Lai
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R. China; E-Mails:
(Z.L.);
(J.S.);
(W.C.)
| | - Jiguo Su
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R. China; E-Mails:
(Z.L.);
(J.S.);
(W.C.)
- College of Science, Yanshan University, Qinhuangdao, 066004, P.R. China
| | - Weizu Chen
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R. China; E-Mails:
(Z.L.);
(J.S.);
(W.C.)
| | - Cunxin Wang
- College of Life Science and Bioengineering, Beijing University of Technology, Beijing, 100124, P.R. China; E-Mails:
(Z.L.);
(J.S.);
(W.C.)
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Etchebest C, Benros C, Bornot A, Camproux AC, de Brevern AG. A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:1059-69. [PMID: 17565494 DOI: 10.1007/s00249-007-0188-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2007] [Revised: 05/05/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
Protein sequence world is considerably larger than structure world. In consequence, numerous non-related sequences may adopt similar 3D folds and different kinds of amino acids may thus be found in similar 3D structures. By grouping together the 20 amino acids into a smaller number of representative residues with similar features, sequence world simplification may be achieved. This clustering hence defines a reduced amino acid alphabet (reduced AAA). Numerous works have shown that protein 3D structures are composed of a limited number of building blocks, defining a structural alphabet. We previously identified such an alphabet composed of 16 representative structural motifs (5-residues length) called Protein Blocks (PBs). This alphabet permits to translate the structure (3D) in sequence of PBs (1D). Based on these two concepts, reduced AAA and PBs, we analyzed the distributions of the different kinds of amino acids and their equivalences in the structural context. Different reduced sets were considered. Recurrent amino acid associations were found in all the local structures while other were specific of some local structures (PBs) (e.g Cysteine, Histidine, Threonine and Serine for the alpha-helix Ncap). Some similar associations are found in other reduced AAAs, e.g Ile with Val, or hydrophobic aromatic residues Trp with Phe and Tyr. We put into evidence interesting alternative associations. This highlights the dependence on the information considered (sequence or structure). This approach, equivalent to a substitution matrix, could be useful for designing protein sequence with different features (for instance adaptation to environment) while preserving mainly the 3D fold.
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Affiliation(s)
- C Etchebest
- Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM UMR-S 726, Université Denis DIDEROT, Paris 7, case 7113, 2, place Jussieu, 75251, Paris, France
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Khatun J, Khare SD, Dokholyan NV. Can Contact Potentials Reliably Predict Stability of Proteins? J Mol Biol 2004; 336:1223-38. [PMID: 15037081 DOI: 10.1016/j.jmb.2004.01.002] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2003] [Revised: 01/08/2004] [Accepted: 01/08/2004] [Indexed: 11/17/2022]
Abstract
The simplest approximation of interaction potential between amino acid residues in proteins is the contact potential, which defines the effective free energy of a protein conformation by a set of amino acid contacts formed in this conformation. Finding a contact potential capable of predicting free energies of protein states across a variety of protein families will aid protein folding and engineering in silico on a computationally tractable time-scale. We test the ability of contact potentials to accurately and transferably (across various protein families) predict stability changes of proteins upon mutations. We develop a new methodology to determine the contact potentials in proteins from experimental measurements of changes in protein's thermodynamic stabilities (DeltaDeltaG) upon mutations. We apply our methodology to derive sets of contact interaction parameters for a hierarchy of interaction models including solvation and multi-body contact parameters. We test how well our models reproduce experimental measurements by statistical tests. We evaluate the maximum accuracy of predictions obtained by using contact potentials and the correlation between parameters derived from different data-sets of experimental (DeltaDeltaG) values. We argue that it is impossible to reach experimental accuracy and derive fully transferable contact parameters using the contact models of potentials. However, contact parameters may yield reliable predictions of DeltaDeltaG for datasets of mutations confined to the same amino acid positions in the sequence of a single protein.
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Affiliation(s)
- Jainab Khatun
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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