1
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Zhao K, Zhao P, Wang S, Xia Y, Zhang G. FoldPAthreader: predicting protein folding pathway using a novel folding force field model derived from known protein universe. Genome Biol 2024; 25:152. [PMID: 38862984 PMCID: PMC11167914 DOI: 10.1186/s13059-024-03291-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/29/2024] [Indexed: 06/13/2024] Open
Abstract
Protein folding has become a tractable problem with the significant advances in deep learning-driven protein structure prediction. Here we propose FoldPAthreader, a protein folding pathway prediction method that uses a novel folding force field model by exploring the intrinsic relationship between protein evolution and folding from the known protein universe. Further, the folding force field is used to guide Monte Carlo conformational sampling, driving the protein chain fold into its native state by exploring potential intermediates. On 30 example targets, FoldPAthreader successfully predicts 70% of the proteins whose folding pathway is consistent with biological experimental data.
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Affiliation(s)
- Kailong Zhao
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Pengxin Zhao
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Suhui Wang
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Yuhao Xia
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China
| | - Guijun Zhang
- College of Information Engineering, Zhejiang University of Technology, HangZhou, 310023, China.
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2
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Jaramillo-Martinez V, Dominguez MJ, Bell GM, Souness ME, Carhart AH, Cuibus MA, Masoumzadeh E, Lantz BJ, Adkins AJ, Latham MP, Ball KA, Stollar EJ. How a highly acidic SH3 domain folds in the absence of its charged peptide target. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.532811. [PMID: 36993259 PMCID: PMC10055188 DOI: 10.1101/2023.03.21.532811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Charged residues on the surface of proteins are critical for both protein stability and interactions. However, many proteins contain binding regions with a high net-charge that may destabilize the protein but are useful for binding to oppositely charged targets. We hypothesized that these domains would be marginally stable, as electrostatic repulsion would compete with favorable hydrophobic collapse during folding. Furthermore, by increasing the salt concentration we predict that these protein folds would be stabilized by mimicking some of the favorable electrostatic interactions that take place during target binding. We varied the salt and urea concentrations to probe the contributions of electrostatic and hydrophobic interactions for the folding of the 60-residue yeast SH3 domain found in Abp1p. The SH3 domain was significantly stabilized with increased salt concentrations according to the Debye-Huckel limiting law. Molecular dynamics and NMR show that sodium ions interact with all 15 acidic residues but do little to change backbone dynamics or overall structure. Folding kinetics experiments show that the addition of urea or salt primarily affects the folding rate, indicating that almost all the hydrophobic collapse and electrostatic repulsion occurs in the transition state. After the transition state formation, modest yet favorable short-range salt-bridges are formed along with hydrogen bonds, as the native state fully folds. Thus, hydrophobic collapse offsets electrostatic repulsion to ensure this highly charged binding domain can still fold and be ready to bind to its charged peptide targets, a property that is likely evolutionarily conserved over one billion years. Statement for broader audience Some protein domains are highly charged because they are adapted to bind oppositely charged proteins and nucleic acids. However, it is unknown how these highly charged domains fold as during folding there will be significant repulsion between like-charges. We investigate how one of these highly charged domains folds in the presence of salt, which can screen the charge repulsion and make folding easier, allowing us to understand how folding occurs despite the protein’s high charge. Supplementary material Supplementary material document containing additional details on protein expression methods, thermodynamics and kinetics equations, and the effect of urea on electrostatic interactions, as well as 4 supplemental figures and 4 supplemental data tables. ( Supplementary_Material.docx ), 15 pages Supplemental excel file containing covariation data across AbpSH3 orthologs ( FileS1.xlsx ).
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3
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Baxa MC, Sosnick TR. Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis. Methods Mol Biol 2022; 2376:31-63. [PMID: 34845602 DOI: 10.1007/978-1-0716-1716-8_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The formation of the transition state ensemble (TSE) represents the rate-limiting step in protein folding. The TSE is the least populated state on the pathway, and its characterization remains a challenge. Properties of the TSE can be inferred from the effects on folding and unfolding rates for various perturbations. A difficulty remains on how to translate these kinetic effects to structural properties of the TSE. Several factors can obscure the translation of point mutations in the frequently used method, "mutational Phi analysis." We take a complementary approach in "Psi analysis," employing rationally inserted metal binding sites designed to probe pairwise contacts in the TSE. These contacts can be confidently identified and used to construct structural models of the TSE. The method has been applied to multiple proteins and consistently produces a considerably more structured and native-like TSE than Phi analysis. This difference has significant implications to our understanding of protein folding mechanisms. Here we describe the application of the method and discuss how it can be used to study other conformational transitions such as binding.
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Affiliation(s)
- Michael C Baxa
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.
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4
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Leader DP, Milner-White EJ. The β-link motif in protein architecture. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2021; 77:1040-1049. [PMID: 34342277 DOI: 10.1107/s2059798321006768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 06/29/2021] [Indexed: 11/10/2022]
Abstract
The β-link is a composite protein motif consisting of a G1β β-bulge and a type II β-turn, and is generally found at the end of two adjacent strands of antiparallel β-sheet. The 1,2-positions of the β-bulge are also the 3,4-positions of the β-turn, with the result that the N-terminal portion of the polypeptide chain is orientated at right angles to the β-sheet. Here, it is reported that the β-link is frequently found in certain protein folds of the SCOPe structural classification at specific locations where it connects a β-sheet to another area of a protein. It is found at locations where it connects one β-sheet to another in the β-sandwich and related structures, and in small (four-, five- or six-stranded) β-barrels, where it connects two β-strands through the polypeptide chain that crosses an open end of the barrel. It is not found in larger (eight-stranded or more) β-barrels that are straightforward β-meanders. In some cases it initiates a connection between a single β-sheet and an α-helix. The β-link also provides a framework for catalysis in serine proteases, where the catalytic serine is part of a conserved β-link, and in cysteine proteases, including Mpro of human SARS-CoV-2, in which two residues of the active site are located in a conserved β-link.
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Affiliation(s)
- David P Leader
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - E James Milner-White
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
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5
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Laursen L, Gianni S, Jemth P. Dissecting Inter-domain Cooperativity in the Folding of a Multi Domain Protein. J Mol Biol 2021; 433:167148. [PMID: 34245784 DOI: 10.1016/j.jmb.2021.167148] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 11/28/2022]
Abstract
Correct protein folding underlies all cellular functions. While there are detailed descriptions and a good understanding of protein folding pathways for single globular domains there is a paucity of quantitative data regarding folding of multidomain proteins. We have here investigated the folding of a three-domain supramodule from the protein PSD-95, consisting of one PDZ domain, one SH3 domain and one guanylate kinase-like (GK) domain. This supramodule has previously been shown to work as one functional unit with regard to ligand binding. We used equilibrium and kinetic folding experiments to demonstrate that the PDZ domain folds faster and independently from the SH3-GK tandem, which folds as one cooperative unit. However, concurrent folding of the PDZ domain slows down folding of SH3-GK by non-native interactions, resulting in an off-pathway folding intermediate. Our data contribute to an emerging description of multidomain protein folding in which individual domains cannot a priori be viewed as separate folding units.
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Affiliation(s)
- Louise Laursen
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden
| | - Stefano Gianni
- Istituto Pasteur-Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli," Sapienza Università di Roma, 00185 Rome, Italy.
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123 Uppsala, Sweden.
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6
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Demakis C, Childers MC, Daggett V. Conserved patterns and interactions in the unfolding transition state across SH3 domain structural homologues. Protein Sci 2020; 30:391-407. [PMID: 33190305 DOI: 10.1002/pro.3998] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 09/30/2020] [Accepted: 11/12/2020] [Indexed: 11/08/2022]
Abstract
Proteins with similar structures are generally assumed to arise from similar sequences. However, there are more cases than not where this is not true. The dogma is that sequence determines structure; how, then, can very different sequences fold to the same structure? Here, we employ high temperature unfolding simulations to probe the pathways and specific interactions that direct the folding and unfolding of the SH3 domain. The SH3 metafold in the Dynameomics Database consists of 753 proteins with the same structure, but varied sequences and functions. To investigate the relationship between sequence and structure, we selected 17 targets from the SH3 metafold with high sequence variability. Six unfolding simulations were performed for each target, transition states were identified, revealing two general folding/unfolding pathways at the transition state. Transition states were also expressed as mathematical graphs of connected chemical nodes, and it was found that three positions within the structure, independent of sequence, were consistently more connected within the graph than any other nearby positions in the sequence. These positions represent a hub connecting different portions of the structure. Multiple sequence alignment and covariation analyses also revealed certain positions that were more conserved due to packing constraints and stabilizing long-range contacts. This study demonstrates that members of the SH3 domain with different sequences can unfold through two main pathways, but certain characteristics are conserved regardless of the sequence or unfolding pathway. While sequence determines structure, we show that disparate sequences can provide similar interactions that influence folding and lead to similar structures.
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Affiliation(s)
- Cullen Demakis
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Matthew C Childers
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, Washington, USA
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7
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de Oliveira VM, Caetano DLZ, da Silva FB, Mouro PR, de Oliveira AB, de Carvalho SJ, Leite VBP. pH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study. J Chem Theory Comput 2020; 16:765-772. [PMID: 31756296 DOI: 10.1021/acs.jctc.9b00894] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The folding and stability of proteins is a fundamental problem in several research fields. In the present paper, we have used different computational approaches to study the effects caused by changes in pH and for charged mutations in cold shock proteins from Bacillus subtilis (Bs-CspB). First, we have investigated the contribution of each ionizable residue for these proteins to their thermal stability using the TKSA-MC, a Web server for rational mutation via optimizing the protein charge interactions. Based on these results, we have proposed a new mutation in an already optimized Bs-CspB variant. We have evaluated the effects of this new mutation in the folding energy landscape using structure-based models in Monte Carlo simulation at constant pH, SBM-CpHMC. Our results using this approach have indicated that the charge rearrangements already in the unfolded state are critical to the thermal stability of Bs-CspB. Furthermore, the conjunction of these simplified methods was able not only to predict stabilizing mutations in different pHs but also to provide essential information about their effects in each stage of protein folding.
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Affiliation(s)
- Vinícius M de Oliveira
- Brazilian Biosciences National Laboratory, National Center for Research in Energy and Materials, LNBio/CNPEM , Campinas , São Paulo , 13083-970 , Brazil
| | - Daniel L Z Caetano
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Fernando B da Silva
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Paulo R Mouro
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Antonio B de Oliveira
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Sidney J de Carvalho
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil
| | - Vitor B P Leite
- Department of Physics , São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences , São José do Rio Preto , São Paulo , 15054-000 , Brazil.,Center for Theoretical Biological Physics , Rice University , Houston , Texas 77005 , United States
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8
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PFDB: A standardized protein folding database with temperature correction. Sci Rep 2019; 9:1588. [PMID: 30733462 PMCID: PMC6367381 DOI: 10.1038/s41598-018-36992-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 11/22/2018] [Indexed: 11/23/2022] Open
Abstract
We constructed a standardized protein folding kinetics database (PFDB) in which the logarithmic rate constants of all listed proteins are calculated at the standard temperature (25 °C). A temperature correction based on the Eyring–Kramers equation was introduced for proteins whose folding kinetics were originally measured at temperatures other than 25 °C. We verified the temperature correction by comparing the logarithmic rate constants predicted and experimentally observed at 25 °C for 14 different proteins, and the results demonstrated improvement of the quality of the database. PFDB consists of 141 (89 two-state and 52 non-two-state) single-domain globular proteins, which has the largest number among the currently available databases of protein folding kinetics. PFDB is thus intended to be used as a standard for developing and testing future predictive and theoretical studies of protein folding. PFDB can be accessed from the following link: http://lee.kias.re.kr/~bala/PFDB.
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9
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Troilo F, Bonetti D, Camilloni C, Toto A, Longhi S, Brunori M, Gianni S. Folding Mechanism of the SH3 Domain from Grb2. J Phys Chem B 2018; 122:11166-11173. [DOI: 10.1021/acs.jpcb.8b06320] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Francesca Troilo
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Daniela Bonetti
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Carlo Camilloni
- Dipartimento di Bioscienze, Università degli studi di Milano, 20133 Milan, Italy
| | - Angelo Toto
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Sonia Longhi
- Aix-Marseille Univ, CNRS, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR, 7257 Marseille, France
| | - Maurizio Brunori
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
| | - Stefano Gianni
- Istituto Pasteur—Fondazione Cenci Bolognetti, Dipartimento di Scienze Biochimiche “A. Rossi Fanelli” and Istituto di Biologia e Patologia Molecolari del CNR, Sapienza Università di Roma, 00185 Rome, Italy
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10
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Zegarra FC, Homouz D, Eliaz Y, Gasic AG, Cheung MS. Impact of hydrodynamic interactions on protein folding rates depends on temperature. Phys Rev E 2018; 97:032402. [PMID: 29776093 PMCID: PMC6080349 DOI: 10.1103/physreve.97.032402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Indexed: 01/04/2023]
Abstract
We investigated the impact of hydrodynamic interactions (HI) on protein folding using a coarse-grained model. The extent of the impact of hydrodynamic interactions, whether it accelerates, retards, or has no effect on protein folding, has been controversial. Together with a theoretical framework of the energy landscape theory (ELT) for protein folding that describes the dynamics of the collective motion with a single reaction coordinate across a folding barrier, we compared the kinetic effects of HI on the folding rates of two protein models that use a chain of single beads with distinctive topologies: a 64-residue α/β chymotrypsin inhibitor 2 (CI2) protein, and a 57-residue β-barrel α-spectrin Src-homology 3 domain (SH3) protein. When comparing the protein folding kinetics simulated with Brownian dynamics in the presence of HI to that in the absence of HI, we find that the effect of HI on protein folding appears to have a "crossover" behavior about the folding temperature. This means that at a temperature greater than the folding temperature, the enhanced friction from the hydrodynamic solvents between the beads in an unfolded configuration results in lowered folding rate; conversely, at a temperature lower than the folding temperature, HI accelerates folding by the backflow of solvent toward the folded configuration of a protein. Additionally, the extent of acceleration depends on the topology of a protein: for a protein like CI2, where its folding nucleus is rather diffuse in a transition state, HI channels the formation of contacts by favoring a major folding pathway in a complex free energy landscape, thus accelerating folding. For a protein like SH3, where its folding nucleus is already specific and less diffuse, HI matters less at a temperature lower than the folding temperature. Our findings provide further theoretical insight to protein folding kinetic experiments and simulations.
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Affiliation(s)
- Fabio C. Zegarra
- Department of Physics, University of Houston, Houston, Texas 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Dirar Homouz
- Department of Physics, University of Houston, Houston, Texas 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
- Khalifa University of Science and Technology, Department of Physics, P.O. Box 127788, Abu Dhabi, United Arab Emirates
| | - Yossi Eliaz
- Department of Physics, University of Houston, Houston, Texas 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Andrei G. Gasic
- Department of Physics, University of Houston, Houston, Texas 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
| | - Margaret S. Cheung
- Department of Physics, University of Houston, Houston, Texas 77204, USA
- Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005, USA
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11
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Differences in the mechanical unfolding pathways of apo- and copper-bound azurins. Sci Rep 2018; 8:1989. [PMID: 29386517 PMCID: PMC5792602 DOI: 10.1038/s41598-018-19755-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023] Open
Abstract
Metalloproteins carry out diverse biological functions including metal transport, electron transfer, and catalysis. At present, the influence of metal cofactors on metalloprotein stability is not well understood. Here, we report the mechanical stability and unfolding pathway of azurin, a cupredoxin family protein with β-barrel topology and type I copper-binding centre. Single-molecule force spectroscopy (SMFS) experiments reveal 2-state and 3-state unfolding pathways for apo-azurin. The intermediate in the 3-state pathway occurs at an unfolding contour length of 7.5 nm from the native state. Steered molecular dynamics (SMD) simulations show that apo-azurin unfolds via a first transition state (TS) where β2Β–β8 and β7–β8 strand pairs rupture to form the intermediate, which subsequently unfolds by the collective rupture of remaining strands. SMFS experiments on holo-azurin exhibit an additional 4-state pathway besides the 2-state and 3-state pathways. The unfolding contour length leading to the first intermediate is 6.7 nm suggesting a sequestration of ~1 nm polypeptide chain length by the copper. SMD simulations reveal atomistic details of the copper sequestration and predict a combined β4–β7 pair and copper coordination sphere rupture to create the third TS in the 4-state pathway. Our systematic studies provide detailed mechanistic insights on modulation of protein mechanical properties by metal-cofactors.
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12
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Evidence for the principle of minimal frustration in the evolution of protein folding landscapes. Proc Natl Acad Sci U S A 2017; 114:E1627-E1632. [PMID: 28196883 DOI: 10.1073/pnas.1613892114] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Theoretical and experimental studies have firmly established that protein folding can be described by a funneled energy landscape. This funneled energy landscape is the result of foldable protein sequences evolving following the principle of minimal frustration, which allows proteins to rapidly fold to their native biologically functional conformations. For a protein family with a given functional fold, the principle of minimal frustration suggests that, independent of sequence, all proteins within this family should fold with similar rates. However, depending on the optimal living temperature of the organism, proteins also need to modulate their thermodynamic stability. Consequently, the difference in thermodynamic stability should be primarily caused by differences in the unfolding rates. To test this hypothesis experimentally, we performed comprehensive thermodynamic and kinetic analyses of 15 different proteins from the thioredoxin family. Eight of these thioredoxins were extant proteins from psychrophilic, mesophilic, or thermophilic organisms. The other seven protein sequences were obtained using ancestral sequence reconstruction and can be dated back over 4 billion years. We found that all studied proteins fold with very similar rates but unfold with rates that differ up to three orders of magnitude. The unfolding rates correlate well with the thermodynamic stability of the proteins. Moreover, proteins that unfold slower are more resistant to proteolysis. These results provide direct experimental support to the principle of minimal frustration hypothesis.
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13
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Herzog FA, Braun L, Schoen I, Vogel V. Improved Side Chain Dynamics in MARTINI Simulations of Protein–Lipid Interfaces. J Chem Theory Comput 2016; 12:2446-58. [DOI: 10.1021/acs.jctc.6b00122] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Florian A. Herzog
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Lukas Braun
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Ingmar Schoen
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
| | - Viola Vogel
- Laboratory of Applied Mechanobiology,
Department of Health Sciences and Technology, ETH Zurich, Vladimir-Prelog-Weg
4, 8093 Zurich, Switzerland
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14
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Crystallographic studies on protein misfolding: Domain swapping and amyloid formation in the SH3 domain. Arch Biochem Biophys 2016; 602:116-126. [PMID: 26924596 DOI: 10.1016/j.abb.2016.02.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 02/19/2016] [Accepted: 02/23/2016] [Indexed: 12/18/2022]
Abstract
Oligomerization by 3D domain swapping is found in a variety of proteins of diverse size, fold and function. In the early 1960s this phenomenon was postulated for the oligomers of ribonuclease A, but it was not until the 1990s that X-ray diffraction provided the first experimental evidence of this special manner of oligomerization. Nowadays, structural information has allowed the identification of these swapped oligomers in over one hundred proteins. Although the functional relevance of this phenomenon is not clear, this alternative folding of protomers into intertwined oligomers has been related to amyloid formation. Studies on proteins that develop 3D domain swapping might provide some clues on the early stages of amyloid formation. The SH3 domain is a small modular domain that has been used as a model to study the basis of protein folding. Among SH3 domains, the c-Src-SH3 domain emerges as a helpful model to study 3D domain swapping and amyloid formation.
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15
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Murciano-Calles J, Güell-Bosch J, Villegas S, Martinez JC. Common features in the unfolding and misfolding of PDZ domains and beyond: the modulatory effect of domain swapping and extra-elements. Sci Rep 2016; 6:19242. [PMID: 26754462 PMCID: PMC4709687 DOI: 10.1038/srep19242] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 12/08/2015] [Indexed: 01/31/2023] Open
Abstract
PDZ domains are protein-protein interaction modules sharing the same structural arrangement. To discern whether they display common features in their unfolding/misfolding behaviour we have analyzed in this work the unfolding thermodynamics, together with the misfolding kinetics, of the PDZ fold using three archetypical examples: the second and third PDZ domains of the PSD95 protein and the Erbin PDZ domain. Results showed that all domains passed through a common intermediate, which populated upon unfolding, and that this in turn drove the misfolding towards worm-like fibrillar structures. Thus, the unfolding/misfolding behaviour appears to be shared within these domains. We have also analyzed how this landscape can be modified upon the inclusion of extra-elements, as it is in the nNOS PDZ domain, or the organization of swapped species, as happens in the second PDZ domain of the ZO2 protein. Although the intermediates still formed upon thermal unfolding, the misfolding was prevented to varying degrees.
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Affiliation(s)
- Javier Murciano-Calles
- Departmento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
| | - Jofre Güell-Bosch
- Department de Bioquímica I Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Sandra Villegas
- Department de Bioquímica I Biologia Molecular, Facultat de Biociències, Universitat Autònoma de Barcelona, Bellaterra 08193, Barcelona, Spain
| | - Jose C Martinez
- Departmento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071, Granada, Spain
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16
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17
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Xia X, Longo LM, Sutherland MA, Blaber M. Evolution of a protein folding nucleus. Protein Sci 2015; 25:1227-40. [PMID: 26610273 DOI: 10.1002/pro.2848] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/10/2015] [Indexed: 12/22/2022]
Abstract
The folding nucleus (FN) is a cryptic element within protein primary structure that enables an efficient folding pathway and is the postulated heritable element in the evolution of protein architecture; however, almost nothing is known regarding how the FN structurally changes as complex protein architecture evolves from simpler peptide motifs. We report characterization of the FN of a designed purely symmetric β-trefoil protein by ϕ-value analysis. We compare the structure and folding properties of key foldable intermediates along the evolutionary trajectory of the β-trefoil. The results show structural acquisition of the FN during gene fusion events, incorporating novel turn structure created by gene fusion. Furthermore, the FN is adjusted by circular permutation in response to destabilizing functional mutation. FN plasticity by way of circular permutation is made possible by the intrinsic C3 cyclic symmetry of the β-trefoil architecture, identifying a possible selective advantage that helps explain the prevalence of cyclic structural symmetry in the proteome.
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Affiliation(s)
- Xue Xia
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
| | - Liam M Longo
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300.,Department of Biological Chemistry, Weizmann Institute of Science, Rehovot, Israel
| | - Mason A Sutherland
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
| | - Michael Blaber
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, 32306-4300
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18
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Three easy pieces. Biochim Biophys Acta Gen Subj 2015; 1860:975-980. [PMID: 26679422 DOI: 10.1016/j.bbagen.2015.12.003] [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: 10/19/2015] [Revised: 11/27/2015] [Accepted: 12/03/2015] [Indexed: 11/20/2022]
Abstract
BACKGROUND Differential scanning calorimetry is a powerful method that provides a complete thermodynamic characterization of the stability of a protein as a function of temperature. There are, however, circumstances that preclude a complete analysis of DSC data. The most common ones are irreversible denaturation transitions or transitions that take place at temperatures that are beyond the temperature limit of the instrument. Even for a protein that undergoes reversible thermal denaturation, the extrapolation of the thermodynamic data to lower temperatures, usually 25°C, may become unreliable due to difficulties in the determination of ΔCp. METHODS The combination of differential scanning calorimetry and isothermal chemical denaturation allows reliable thermodynamic analysis of protein stability under less than ideal conditions. RESULTS AND CONCLUSIONS This paper demonstrates how DSC can be used in combination with chemical denaturation to address three different scenarios: 1) estimation of an accurate ΔCp value for a reversible denaturation using as a test system the envelope HIV-1 glycoprotein gp120; 2) determination of the Gibbs energy of stability in the region in which thermal denaturation is irreversible using HEW lysozyme at different pH values; and, 3) determination of Gibbs energy of stability for a thermostable protein, thermolysin.
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19
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Co-evolutionary constraints of globular proteins correlate with their folding rates. FEBS Lett 2015; 589:2179-85. [DOI: 10.1016/j.febslet.2015.06.032] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/09/2015] [Accepted: 06/24/2015] [Indexed: 11/20/2022]
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20
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Modulation of intracellular protein activity at level of protein folding by beta-turn engineering. BIOTECHNOL BIOPROC E 2014. [DOI: 10.1007/s12257-014-0162-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Pedersen SW, Hultqvist G, Strømgaard K, Jemth P. The role of backbone hydrogen bonds in the transition state for protein folding of a PDZ domain. PLoS One 2014; 9:e95619. [PMID: 24748272 PMCID: PMC3991670 DOI: 10.1371/journal.pone.0095619] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 03/27/2014] [Indexed: 12/24/2022] Open
Abstract
Backbone hydrogen bonds are important for the structure and stability of proteins. However, since conventional site-directed mutagenesis cannot be applied to perturb the backbone, the contribution of these hydrogen bonds in protein folding and stability has been assessed only for a very limited set of small proteins. We have here investigated effects of five amide-to-ester mutations in the backbone of a PDZ domain, a 90-residue globular protein domain, to probe the influence of hydrogen bonds in a β-sheet for folding and stability. The amide-to-ester mutation removes NH-mediated hydrogen bonds and destabilizes hydrogen bonds formed by the carbonyl oxygen. The overall stability of the PDZ domain generally decreased for all amide-to-ester mutants due to an increase in the unfolding rate constant. For this particular region of the PDZ domain, it is therefore clear that native hydrogen bonds are formed after crossing of the rate-limiting barrier for folding. Moreover, three of the five amide-to-ester mutants displayed an increase in the folding rate constant suggesting that the hydrogen bonds are involved in non-native interactions in the transition state for folding.
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Affiliation(s)
- Søren W. Pedersen
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Greta Hultqvist
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- * E-mail: (KS); (PJ)
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, Biomedical Center, Uppsala, Sweden
- * E-mail: (KS); (PJ)
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22
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Madan B, Seo SY, Lee SG. Structural and sequence features of two residue turns in beta-hairpins. Proteins 2014; 82:1721-33. [PMID: 24488781 DOI: 10.1002/prot.24526] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2013] [Revised: 01/17/2014] [Accepted: 01/28/2014] [Indexed: 12/16/2022]
Abstract
Beta-turns in beta-hairpins have been implicated as important sites in protein folding. In particular, two residue β-turns, the most abundant connecting elements in beta-hairpins, have been a major target for engineering protein stability and folding. In this study, we attempted to investigate and update the structural and sequence properties of two residue turns in beta-hairpins with a large data set. For this, 3977 beta-turns were extracted from 2394 nonhomologous protein chains and analyzed. First, the distribution, dihedral angles and twists of two residue turn types were determined, and compared with previous data. The trend of turn type occurrence and most structural features of the turn types were similar to previous results, but for the first time Type II turns in beta-hairpins were identified. Second, sequence motifs for the turn types were devised based on amino acid positional potentials of two-residue turns, and their distributions were examined. From this study, we could identify code-like sequence motifs for the two residue beta-turn types. Finally, structural and sequence properties of beta-strands in the beta-hairpins were analyzed, which revealed that the beta-strands showed no specific sequence and structural patterns for turn types. The analytical results in this study are expected to be a reference in the engineering or design of beta-hairpin turn structures and sequences.
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Affiliation(s)
- Bharat Madan
- Department of Chemical Engineering, Pusan National University, Busan, 609-735, South Korea
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23
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Ruzafa D, Varela L, Azuaga AI, Conejero-Lara F, Morel B. Mapping the structure of amyloid nucleation precursors by protein engineering kinetic analysis. Phys Chem Chem Phys 2014; 16:2989-3000. [PMID: 24394436 DOI: 10.1039/c3cp54383h] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Understanding the early molecular mechanisms governing amyloid aggregation is crucial to learn how to prevent it. Here, we used a site-directed mutagenesis approach to explore the molecular mechanism of nucleation of amyloid structure in the N47A Spc-SH3 domain. The changes in the native state stability produced by a series of mutations on each structural element of the domain were uncorrelated with the changes in the aggregation rates, although the overall aggregation mechanism was not altered. Analysis of the thioflavin T initial rates based on a simple kinetic model allowed us to extract thermodynamic magnitudes of the precursor states of nucleation and map the regions of the protein participating in the structure of the amyloidogenic precursors. This structure differs from that of the folding transition state of the SH3 domains, strongly suggesting that the regions of the conformational landscape leading to amyloid formation are divergent from those leading to the native fold.
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Affiliation(s)
- David Ruzafa
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, 18071 Granada, Spain.
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24
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Assessing the effect of loop mutations in the folding space of β2-microglobulin with molecular dynamics simulations. Int J Mol Sci 2013; 14:17256-78. [PMID: 23975166 PMCID: PMC3794727 DOI: 10.3390/ijms140917256] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 07/27/2013] [Accepted: 07/30/2013] [Indexed: 12/15/2022] Open
Abstract
We use molecular dynamics simulations of a full atomistic Gō model to explore the impact of selected DE-loop mutations (D59P and W60C) on the folding space of protein human β2-microglobulin (Hβ2m), the causing agent of dialysis-related amyloidosis, a conformational disorder characterized by the deposition of insoluble amyloid fibrils in the osteoarticular system. Our simulations replicate the effect of mutations on the thermal stability that is observed in experiments in vitro. Furthermore, they predict the population of a partially folded state, with 60% of native internal free energy, which is akin to a molten globule. In the intermediate state, the solvent accessible surface area increases up to 40 times relative to the native state in 38% of the hydrophobic core residues, indicating that the identified species has aggregation potential. The intermediate state preserves the disulfide bond established between residue Cys25 and residue Cys80, which helps maintain the integrity of the core region, and is characterized by having two unstructured termini. The movements of the termini dominate the essential modes of the intermediate state, and exhibit the largest displacements in the D59P mutant, which is the most aggregation prone variant. PROPKA predictions of pKa suggest that the population of the intermediate state may be enhanced at acidic pH explaining the larger amyloidogenic potential observed in vitro at low pH for the WT protein and mutant forms.
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25
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Dony N, Crowet JM, Joris B, Brasseur R, Lins L. SAHBNET, an accessible surface-based elastic network: an application to membrane protein. Int J Mol Sci 2013; 14:11510-26. [PMID: 23722660 PMCID: PMC3709745 DOI: 10.3390/ijms140611510] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 05/02/2013] [Accepted: 05/20/2013] [Indexed: 11/06/2022] Open
Abstract
Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins.
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Affiliation(s)
- Nicolas Dony
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Jean Marc Crowet
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Bernard Joris
- Center of Protein Engineering, University of Liège, Institut de chimie B6a, B-4000 Liège, Belgium; E-Mails: (N.D.); (B.J.)
| | - Robert Brasseur
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
| | - Laurence Lins
- Numerical Molecular Biophysics Unit, Gembloux Agro-Bio Tech, University of Liège, Passage des déportés, B-5030 Gembloux, Belgium; E-Mails: (J.M.C.); (R.B.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +32-81-622-521; Fax: +32-81-622-522
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26
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Scian M, Shu I, Olsen KA, Hassam K, Andersen NH. Mutational effects on the folding dynamics of a minimized hairpin. Biochemistry 2013; 52:2556-64. [PMID: 23521619 DOI: 10.1021/bi400146c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The fold stabilities and folding dynamics of a series of mutants of a model hairpin, KTW-NPATGK-WTE (HP7), are reported. The parent system and the corresponding DPATGK loop species display submicrosecond folding time constants. The mutational studies revealed that ultrafast folding requires both some prestructuring of the loop and a favorable interaction between the chain termini in the transition state. In the case of YY-DPETGT-WY, another submicrosecond folding species [Davis, C. M., Xiao, S., Raleigh, D. P., and Dyer, R. B. (2012) J. Am. Chem. Soc. 134, 14476-14482], a hydrophobic cluster provides the latter. In the case of HP7, the Coulombic interaction between the terminal NH3(+) and CO2(-) units provides this; a C-terminal Glu to amidated Ala mutation results in a 5-fold retardation of the folding rate. The effects of mutations within the reversing loop indicate the balance between loop flexibility (favoring fast conformational searching) and turn formation in the unfolded state is a major factor in determining the folding dynamics. The -NAAAKX- loops examined display no detectable turn formation propensity in other hairpin constructs but do result in stable analogues of HP7. Peptide KTW-NAAAKK-WTE displays the same fold stability as HP7, but both the folding and unfolding time constants are greater by a factor of 20.
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Affiliation(s)
- Michele Scian
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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27
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Torshin IY, Esipova NG, Tumanyan VG. Alternatingly twisted β-hairpins and nonglycine residues in the disallowed II′ region of the Ramachandran plot. J Biomol Struct Dyn 2013; 32:198-208. [DOI: 10.1080/07391102.2012.759451] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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28
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Mohazab AR, Plotkin SS. Polymer uncrossing and knotting in protein folding, and their role in minimal folding pathways. PLoS One 2013; 8:e53642. [PMID: 23365638 PMCID: PMC3554774 DOI: 10.1371/journal.pone.0053642] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 11/30/2012] [Indexed: 11/19/2022] Open
Abstract
We introduce a method for calculating the extent to which chain non-crossing is important in the most efficient, optimal trajectories or pathways for a protein to fold. This involves recording all unphysical crossing events of a ghost chain, and calculating the minimal uncrossing cost that would have been required to avoid such events. A depth-first tree search algorithm is applied to find minimal transformations to fold [Formula: see text], [Formula: see text], [Formula: see text], and knotted proteins. In all cases, the extra uncrossing/non-crossing distance is a small fraction of the total distance travelled by a ghost chain. Different structural classes may be distinguished by the amount of extra uncrossing distance, and the effectiveness of such discrimination is compared with other order parameters. It was seen that non-crossing distance over chain length provided the best discrimination between structural and kinetic classes. The scaling of non-crossing distance with chain length implies an inevitable crossover to entanglement-dominated folding mechanisms for sufficiently long chains. We further quantify the minimal folding pathways by collecting the sequence of uncrossing moves, which generally involve leg, loop, and elbow-like uncrossing moves, and rendering the collection of these moves over the unfolded ensemble as a multiple-transformation "alignment". The consensus minimal pathway is constructed and shown schematically for representative cases of an [Formula: see text], [Formula: see text], and knotted protein. An overlap parameter is defined between pathways; we find that [Formula: see text] proteins have minimal overlap indicating diverse folding pathways, knotted proteins are highly constrained to follow a dominant pathway, and [Formula: see text] proteins are somewhere in between. Thus we have shown how topological chain constraints can induce dominant pathway mechanisms in protein folding.
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Affiliation(s)
- Ali R. Mohazab
- Department of Physics and Astronomy, University of British Columbia, Vancouver, B.C, Canada
| | - Steven S. Plotkin
- Department of Physics and Astronomy, University of British Columbia, Vancouver, B.C, Canada
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29
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Dasgupta A, Udgaonkar JB. Transient Non-Native Burial of a Trp Residue Occurs Initially during the Unfolding of a SH3 Domain. Biochemistry 2012; 51:8226-34. [DOI: 10.1021/bi3008627] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Amrita Dasgupta
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
| | - Jayant B. Udgaonkar
- National Centre for Biological
Sciences, Tata Institute of Fundamental Research, Bangalore 560065,
India
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30
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Krobath H, Estácio S, Faísca P, Shakhnovich E. Identification of a Conserved Aggregation-Prone Intermediate State in the Folding Pathways of Spc-SH3 Amyloidogenic Variants. J Mol Biol 2012; 422:705-722. [DOI: 10.1016/j.jmb.2012.06.020] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 06/11/2012] [Accepted: 06/11/2012] [Indexed: 01/30/2023]
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31
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Joseph AP, Valadié H, Srinivasan N, de Brevern AG. Local structural differences in homologous proteins: specificities in different SCOP classes. PLoS One 2012; 7:e38805. [PMID: 22745680 PMCID: PMC3382195 DOI: 10.1371/journal.pone.0038805] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Accepted: 05/10/2012] [Indexed: 11/19/2022] Open
Abstract
The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions.
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Affiliation(s)
- Agnel Praveen Joseph
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR 665, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
| | - Hélène Valadié
- INSERM UMR-S 726, DSIMB, Université Paris Diderot - Paris 7, Paris, France
| | | | - Alexandre G. de Brevern
- INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Paris, France
- Univ Paris Diderot, Sorbonne Paris Cité, UMR 665, Paris, France
- Institut National de la Transfusion Sanguine (INTS), Paris, France
- * E-mail:
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32
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Interfacial water molecules in SH3 interactions: Getting the full picture on polyproline recognition by protein-protein interaction domains. FEBS Lett 2012; 586:2619-30. [DOI: 10.1016/j.febslet.2012.04.057] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Revised: 04/27/2012] [Accepted: 04/30/2012] [Indexed: 01/16/2023]
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33
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Shandiz AT, Baxa MC, Sosnick TR. A "Link-Psi" strategy using crosslinking indicates that the folding transition state of ubiquitin is not very malleable. Protein Sci 2012; 21:819-27. [PMID: 22528473 DOI: 10.1002/pro.2065] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2012] [Revised: 03/19/2012] [Accepted: 03/19/2012] [Indexed: 11/09/2022]
Abstract
Using a combined crosslinking-ψ analysis strategy, we examine whether the structural content of the transition state of ubiquitin can be altered. A synthetic dichloroacetone crosslink is first introduced across two β strands. Whether the structural content in the transition state ensemble has shifted towards the region containing the crosslink is probed by remeasuring the ψ value at another region (ψ identifies the degree to which an inserted bi-Histidine metal ion binding site is formed in the transition state). For sites around the periphery of the obligate transition state nucleus, we find that the resulting changes in ψ values are near or at our detection limit, thereby indicating that the structural content of the transition state has not measurably changed upon crosslinking. This work demonstrates the utility of the simultaneous application of crosslinking and ψ-analysis for examining potential transition state heterogeneity in globular proteins.
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Affiliation(s)
- Ali T Shandiz
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, Illinois 60637, USA
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34
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Duclert-Savatier N, Martínez L, Nilges M, Malliavin TE. The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations. BMC STRUCTURAL BIOLOGY 2011; 11:46. [PMID: 22115427 PMCID: PMC3274457 DOI: 10.1186/1472-6807-11-46] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2011] [Accepted: 11/24/2011] [Indexed: 11/29/2022]
Abstract
1 Abstract
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Affiliation(s)
- Nathalie Duclert-Savatier
- Institut Pasteur, CNRS URA 2185, Unité de Bioinformatique Structurale, 25-28 rue du Dr Roux, F-75724 Paris Cedex 15, France
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35
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Yuwen T, Post CB, Skrynnikov N. Domain cooperativity in multidomain proteins: what can we learn from molecular alignment in anisotropic media? JOURNAL OF BIOMOLECULAR NMR 2011; 51:131-50. [PMID: 21947922 PMCID: PMC4721247 DOI: 10.1007/s10858-011-9548-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2011] [Accepted: 07/07/2011] [Indexed: 05/13/2023]
Abstract
Many proteins have modular design with multiple globular domains connected via flexible linkers. As a simple model of such system, we study a tandem construct consisting of two identical SH3 domains and a variable-length Gly/Ser linker. When the linker is short, this construct represents a dumbbell-shaped molecule with limited amount of domain-domain mobility. Due to its elongated shape, this molecule efficiently aligns in steric alignment media. As the length of the linker increases, the two domains become effectively uncoupled and begin to behave as independent entities. Consequently, their degree of alignment drops, approaching that found in the (near-spherical) isolated SH3 domains. To model the dependence of alignment parameters on the length of the interdomain linker, we have generated in silico a series of conformational ensembles representing SH3 tandems with different linker length. These ensembles were subsequently used as input for alignment prediction software PALES. The predicted alignment tensors were compared with the results of experimental measurements using a series of tandem-SH3 samples in PEG/hexanol alignment media. This comparison broadly confirmed the expected trends. At the same time, it has been found that the isolated SH3 domain aligns much stronger than expected. This finding can be attributed to complex morphology of the PEG/hexanol media and/or to weak site-specific interactions between the protein and the media. In the latter case, there are strong indications that electrostatic interactions may play a role. The fact that PEG/hexanol does not behave as a simple steric media should serve as a caution for studies that use PALES as a quantitative prediction tool (especially for disordered proteins). Further progress in this area depends on our ability to accurately model the anisotropic media and its site-specific interactions with protein molecules. Once this ability is improved, it should be possible to use the alignment parameters as a measure of domain-domain cooperativity, thus identifying the situations where two domains transiently interact with each other or become coupled through a partially structured linker.
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Affiliation(s)
- Tairan Yuwen
- Department of Chemistry, Purdue University, West Lafayette IN 47907, USA
| | - Carol Beth Post
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette IN 47907, USA
| | - Nikolai Skrynnikov
- Department of Chemistry, Purdue University, West Lafayette IN 47907, USA
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36
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Tian XH, Zheng YH, Jiao X, Liu CX, Chang S. Computational model for protein unfolding simulation. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 83:061910. [PMID: 21797406 DOI: 10.1103/physreve.83.061910] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2010] [Revised: 03/11/2011] [Indexed: 05/31/2023]
Abstract
The protein folding problem is one of the fundamental and important questions in molecular biology. However, the all-atom molecular dynamics studies of protein folding and unfolding are still computationally expensive and severely limited by the time scale of simulation. In this paper, a simple and fast protein unfolding method is proposed based on the conformational stability analyses and structure modeling. In this method, two structure-based conditions are considered to identify the unstable regions of proteins during the unfolding processes. The protein unfolding trajectories are mimicked through iterative structure modeling according to conformational stability analyses. Two proteins, chymotrypsin inhibitor 2 (CI2) and α -spectrin SH3 domain (SH3) were simulated by this method. Their unfolding pathways are consistent with the previous molecular dynamics simulations. Furthermore, the transition states of the two proteins were identified in unfolding processes and the theoretical Φ values of these transition states showed significant correlations with the experimental data (the correlation coefficients are >0.8). The results indicate that this method is effective in studying protein unfolding. Moreover, we analyzed and discussed the influence of parameters on the unfolding simulation. This simple coarse-grained model may provide a general and fast approach for the mechanism studies of protein folding.
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Affiliation(s)
- Xu-hong Tian
- College of Informatics, South China Agricultural University, Guangzhou, China
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37
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Buck PM, Bystroff C. Constraining local structure can speed up folding by promoting structural polarization of the folding pathway. Protein Sci 2011; 20:959-69. [PMID: 21413096 DOI: 10.1002/pro.619] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2010] [Revised: 02/20/2011] [Accepted: 02/22/2011] [Indexed: 11/08/2022]
Abstract
The pathway which proteins take to fold can be influenced from the earliest events of structure formation. In this light, it was both predicted and confirmed that increasing the stiffness of a beta hairpin turn decreased the size of the transition state ensemble (TSE), while increasing the folding rate. Thus, there appears to be a relationship between conformationally restricting the TSE and increasing the folding rate, at least for beta hairpin turns. In this study, we hypothesize that the enormous sampling necessary to fold even two-state folding proteins in silico could be reduced if local structure constraints were used to restrict structural heterogeneity by polarizing folding pathways or forcing folding into preferred routes. Using a Gō model, we fold Chymotrypsin Inhibitor 2 (CI-2) and the src SH3 domain after constraining local sequence windows to their native structure by rigid body dynamics (RBD). Trajectories were monitored for any changes to the folding pathway and differences in the kinetics compared with unconstrained simulations. Constraining local structure decreases folding time two-fold for 41% of src SH3 windows and 45% of CI-2 windows. For both proteins, folding times are never significantly increased after constraining any window. Structural polarization of the folding pathway appears to explain these rate increases. Folding rate enhancements are consistent with the goal to reduce sampling time necessary to reach native structures during folding simulations. As anticipated, not all constrained windows showed an equal decrease in folding time. We conclude by analyzing these differences and explain why RBD may be the preferred way to constrain structure.
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Affiliation(s)
- Patrick M Buck
- Department of Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, USA
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38
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Morel B, Varela L, Azuaga AI, Conejero-Lara F. Environmental conditions affect the kinetics of nucleation of amyloid fibrils and determine their morphology. Biophys J 2011; 99:3801-10. [PMID: 21112305 DOI: 10.1016/j.bpj.2010.10.039] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2010] [Revised: 10/22/2010] [Accepted: 10/25/2010] [Indexed: 01/09/2023] Open
Abstract
To understand and tackle amyloid-related diseases, it is crucial to investigate the factors that modulate amyloid formation of proteins. Our previous studies proved that the N47A mutant of the α-spectrin SH3 (Spc-SH3) domain forms amyloid fibrils quickly under mildly acidic conditions. Here, we analyze how experimental conditions influence the kinetics of assembly and the final morphology of the fibrils. Early formation of curly fibrils occurs after a considerable conformational change of the protein and the concomitant formation of small oligomers. These processes are strongly accelerated by an increase in salt concentration and temperature, and to a lesser extent by a reduction in pH. The rate-limiting step in these events has a high activation enthalpy, which is significantly reduced by an increase in NaCl concentration. At low-to-moderate NaCl concentrations, the curly fibrils convert to straight and twisted amyloid fibrils after long incubation times, but only in the presence of soluble species in the mixture, which suggests that the curly fibrils and the twisted amyloid fibrils are diverging assembly pathways. The results suggest that the influence of environmental variables on protein solvation is crucial in determining the nucleation kinetics, the pathway of assembly, and the final fibril morphology.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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39
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Castillo V, Espargaró A, Gordo V, Vendrell J, Ventura S. Deciphering the role of the thermodynamic and kinetic stabilities of SH3 domains on their aggregation inside bacteria. Proteomics 2011; 10:4172-85. [PMID: 21086517 DOI: 10.1002/pmic.201000260] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
The formation of insoluble deposits by globular proteins underlies the onset of many human diseases. Recent studies suggest a relationship between the thermodynamic stability of proteins and their in vivo aggregation. However, it has been argued that, in the cell, the occurrence of irreversible aggregation might shift the system from equilibrium, in such a way that it could be the rate of unfolding and associated kinetic stability instead of the conformational stability that controls protein deposition. This is an important but difficult to decipher question, because kinetic and thermodynamic stabilities appear usually correlated. Here we address this issue by comparing the in vitro folding kinetics and stability features of a set of non-natural SH3 domains with their aggregation properties when expressed in bacteria. In addition, we compare the in vitro stability of the isolated domains with their effective stability in conditions that mimic the cytosolic environment. Overall, the data argue in favor of a thermodynamic rather than a kinetic control of the intracellular aggregation propensities of small globular proteins in which folding and unfolding velocities largely exceed aggregation rates. These results have implications regarding the evolution of proteins.
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Affiliation(s)
- Virginia Castillo
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra (Barcelona), Spain
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40
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Chen Y, Ding J. Roles of non-native hydrogen-bonding interaction in helix-coil transition of a single polypeptide as revealed by comparison between Gō-like and non-Gō models. Proteins 2010; 78:2090-100. [PMID: 20455265 DOI: 10.1002/prot.22724] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
To explore the role of non-native interactions in the helix-coil transition, a detailed comparison between a Gō-like model and a non-Gō model has been performed via lattice Monte Carlo simulations. Only native hydrogen bonding interactions occur in the Gō-like model, and the non-native ones with sequence interval more than 4 is also included into the non-Gō model. Some significant differences between the results from those two models have been found. The non-native hydrogen bonds were found most populated at temperature around the helix-coil transition. The rearrangement of non-native hydrogen bonds into native ones in the formation of alpha-helix leads to the increase of susceptibility of chain conformation, and even two peaks of susceptibility of radius of gyration versus temperature exist in the case of non-Gō model for a non-short peptide, while just a single peak exists in the case of Gō model for a single polypeptide chain with various chain lengths. The non-native hydrogen bonds have complicated the temperature-dependence of Zimm-Bragg nucleation constant. The increase of relative probability of non-native hydrogen bonding for long polypeptide chains leads to non-monotonous chain length effect on the transition temperature.
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Affiliation(s)
- Yantao Chen
- Key Laboratory of Molecular Engineering of Polymers of Ministry of Education, Department of Macromolecular Science, Laboratory of Advanced Materials, Fudan University, Shanghai 200433, China
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41
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Investigation of an anomalously accelerating substitution in the folding of a prototypical two-state protein. J Mol Biol 2010; 403:446-58. [PMID: 20816985 DOI: 10.1016/j.jmb.2010.08.049] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2010] [Revised: 08/26/2010] [Accepted: 08/27/2010] [Indexed: 11/22/2022]
Abstract
The folding rates of two-state single-domain proteins are generally resistant to small-scale changes in amino acid sequence. For example, having surveyed here over 700 single-residue substitutions in 24 well-characterized two-state proteins, we find that the majority (55%) of these substitutions affect folding rates by less than a factor of 2, and that only 9% affect folding rates by more than a factor of 8. Among those substitutions that significantly affect folding rates, we find that accelerating substitutions are an order of magnitude less common than those that decelerate the process. One of the most extreme outliers in this data set, an arginine-to-phenylalanine substitution at position 48 (R48F) of chymotrypsin inhibitor 2 (CI2), accelerates the protein's folding rate by a factor of 36 relative to that of the wild-type protein and is the most accelerating substitution reported to date in a two-state protein. In order to better understand the origins of this anomalous behavior, we have characterized the kinetics of multiple additional substitutions at this position. We find that substitutions at position 48 in CI2 fall into two distinct classes. The first, comprising residues that ablate the charge of the wild-type arginine but retain the hydrophobicity of its alkane chain, accelerate folding by at least 10-fold. The second class, comprising all other residues, produces folding rates within a factor of two of the wild-type rate. A significant positive correlation between hydrophobicity and folding rate across all of the residues we have characterized at this position suggests that the hydrophobic methylene units of the wild-type arginine play a significant role in stabilizing the folding transition state. Likewise, studies of the pH dependence of the histidine substitution indicate a strong correlation between folding rate and charge state. Thus, mutations that ablate the arginine's positive charge while retaining the hydrophobic contacts of its methylene units tend to dramatically accelerate folding. Previous studies have suggested that arginine 48 plays an important functional role in CI2, which may explain why it is highly conserved despite the anomalously large deceleration it produces in the folding of this protein.
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Cámara-Artigas A, Andújar-Sánchez M, Ortiz-Salmerón E, Cuadri C, Cobos ES, Martin-Garcia JM. High-resolution structure of an alpha-spectrin SH3-domain mutant with a redesigned hydrophobic core. Acta Crystallogr Sect F Struct Biol Cryst Commun 2010; 66:1023-7. [PMID: 20823517 PMCID: PMC2935218 DOI: 10.1107/s1744309110030095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2010] [Accepted: 07/28/2010] [Indexed: 11/10/2022]
Abstract
The alpha-spectrin SH3 domain (Spc-SH3) is a small modular domain which has been broadly used as a model protein in folding studies and these studies have sometimes been supported by structural information obtained from the coordinates of Spc-SH3 mutants. The structure of B5/D48G, a multiple mutant designed to improve the hydrophobic core and as a consequence the protein stability, has been solved at 1 A resolution. The crystals belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=24.79, b=37.23, c=62.95 A. This mutant also bears a D48G substitution in the distal loop and this mutation has also been reported to increase the stability of the protein by itself. The structure of the B5/D48G mutant shows a highly packed hydrophobic core and a more ordered distal loop compared with previous Spc-SH3 structures.
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Affiliation(s)
- Ana Cámara-Artigas
- Departamento de Química-Física, Bioquímica y Química Inorgánica, Universidad de Almería, Carretera Sacramento, Almería 04120, Spain.
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43
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Khristoforov VS, Prokhorov DA, Timchenko MA, Kudrevatykh YA, Gushchina LV, Filimonov VV, Kutyshenko VP. Chimeric SHA-D domain “SH3-Bergerac“: 3D structure and dynamics studies. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2010. [DOI: 10.1134/s1068162010040059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Chevelkov V, Xue Y, Linser R, Skrynnikov NR, Reif B. Comparison of solid-state dipolar couplings and solution relaxation data provides insight into protein backbone dynamics. J Am Chem Soc 2010; 132:5015-7. [PMID: 20297847 DOI: 10.1021/ja100645k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Analyses of solution (15)N relaxation data and solid-state (1)H(N)-(15)N dipolar couplings from a small globular protein, alpha-spectrin SH3 domain, produce a surprisingly similar pattern of order parameters. This result suggests that there is little or no ns-mus dynamics throughout most of the sequence and, in particular, in the structured portion of the backbone. At the same time, evidence of ns-mus motions is found in the flexible loops and termini. These findings, corroborated by the MD simulations of alpha-spectrin SH3 in a hydrated crystalline environment and in solution, are consistent with the picture of protein dynamics that has recently emerged from the solution studies employing residual dipolar couplings.
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Affiliation(s)
- Veniamin Chevelkov
- Forschunginstitut fur Molekulare Pharmakologie (FMP), Robert-Rossle-Strasse 10, 13125 Berlin, Germany
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45
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Thukral L, Smith JC, Daidone I. Common folding mechanism of a beta-hairpin peptide via non-native turn formation revealed by unbiased molecular dynamics simulations. J Am Chem Soc 2010; 131:18147-52. [PMID: 19919102 DOI: 10.1021/ja9064365] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The folding of a 15-residue beta-hairpin peptide (Peptide 1) is characterized using multiple unbiased, atomistic molecular dynamics (MD) simulations. Fifteen independent MD trajectories, each 2.5 micros-long for a total of 37.5 micros, are performed of the peptide in explicit solvent, at room temperature, and without the use of enhanced sampling techniques. The computed folding time of 1-1.5 micros obtained from the simulations is in good agreement with experiment [Xu, Y.; et al. J. Am. Chem. Soc. 2003, 125, 15388-15394]. A common folding mechanism is observed, in which the turn is always found to be the major determinant in initiating the folding process, followed by cooperative formation of the interstrand hydrogen bonds and the side-chain packing. Furthermore, direct transition to the folded state from fully unstructured conformations does not take place. Instead, the peptide is always observed to form partially structured conformations involving a non-native (ESYI) turn from which the native (NPDG) turn forms, triggering the folding to the beta-hairpin.
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Affiliation(s)
- Lipi Thukral
- Interdisciplinary Center for Scientific Computing, University of Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
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46
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Insights into protein aggregation by NMR characterization of insoluble SH3 mutants solubilized in salt-free water. PLoS One 2009; 4:e7805. [PMID: 19956763 PMCID: PMC2776303 DOI: 10.1371/journal.pone.0007805] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2009] [Accepted: 10/16/2009] [Indexed: 12/02/2022] Open
Abstract
Protein aggregation in vivo has been extensively associated with a large spectrum of human diseases. On the other hand, mechanistic insights into protein aggregation in vitro were incomplete due to the inability in solubilizing insoluble proteins for high-resolution biophysical investigations. However, a new avenue may be opened up by our recent discovery that previously-thought insoluble proteins can in fact be solubilized in salt-free water. Here we use this approach to study the NMR structural and dynamic properties of an insoluble SH3 mutant with a naturally-occurring insertion of Val22 at the tip of the diverging turn. The obtained results reveal: 1) regardless of whether the residue is Val, Ala, Asp or Arg, the insertion will render the first hNck2 SH3 domain to be insoluble in buffers. Nevertheless, all four mutants could be solubilized in salt-free water and appear to be largely unfolded as evident from their CD and NMR HSQC spectra. 2) Comparison of the chemical shift deviations reveals that while in V22-SH3 the second helical region is similarly populated as in the wild-type SH3 at pH 2.0, the first helical region is largely unformed. 3) In V22-SH3, many non-native medium-range NOEs manifest to define non-native helical conformations. In the meanwhile a small group of native-like long-range NOEs still persists, indicating the existence of a rudimentary native-like tertiary topology. 4) Although overall, V22-SH3 has significantly increased backbone motions on the ps-ns time scale, some regions still own restricted backbone motions as revealed by analyzing 15N relaxation data. Our study not only leads to the establishment of the first high-resolution structural and dynamic picture for an insoluble protein, but also shed more light on the molecular events for the nonhierarchical folding mechanism. Furthermore, a general mechanism is also proposed for in vivo protein aggregation triggered by the genetic mutation and posttranslational modification.
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47
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Chevelkov V, Fink U, Reif B. Quantitative analysis of backbone motion in proteins using MAS solid-state NMR spectroscopy. JOURNAL OF BIOMOLECULAR NMR 2009; 45:197-206. [PMID: 19629713 DOI: 10.1007/s10858-009-9348-5] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2009] [Accepted: 06/26/2009] [Indexed: 05/13/2023]
Abstract
We present a comprehensive analysis of protein dynamics for a micro-crystallin protein in the solid-state. Experimental data include (15)N T (1) relaxation times measured at two different magnetic fields as well as (1)H-(15)N dipole, (15)N CSA cross correlated relaxation rates which are sensitive to the spectral density function J(0) and are thus a measure of T (2) in the solid-state. In addition, global order parameters are included from a (1)H,(15)N dipolar recoupling experiment. The data are analyzed within the framework of the extended model-free Clore-Lipari-Szabo theory. We find slow motional correlation times in the range of 5 and 150 ns. Assuming a wobbling in a cone motion, the amplitude of motion of the respective amide moiety is on the order of 10 degrees for the half-opening angle of the cone in most of the cases. The experiments are demonstrated using a perdeuterated sample of the chicken alpha-spectrin SH3 domain.
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Affiliation(s)
- Veniamin Chevelkov
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Robert-Rössle-Strasse 10, Berlin, Germany
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48
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Periole X, Cavalli M, Marrink SJ, Ceruso MA. Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition. J Chem Theory Comput 2009; 5:2531-43. [PMID: 26616630 DOI: 10.1021/ct9002114] [Citation(s) in RCA: 456] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies. Here, we study how both approaches can be combined into a single representation, that we term ELNEDIN. In this representation an elastic network is used as a structural scaffold to describe and maintain the overall shape of a protein and a physics-based coarse-grained model (MARTINI-2.1) is used to describe both inter- and intramolecular interactions in the system. The results show that when used in molecular dynamics simulations ELNEDIN models can be built so that the resulting structural and dynamical properties of a protein, including its collective motions, are comparable to those obtained using atomistic protein models. We then evaluate the behavior of such models in (1) long, microsecond time-scale, simulations, (2) the modeling of very large macromolecular assemblies, a viral capsid, and (3) the study of a protein-protein association process, the reassembly of the ROP homodimer. The results for this series of tests indicate that ELNEDIN models allow microsecond time-scale molecular dynamics simulations to be carried out readily, that large biological entities such as the viral capsid of the cowpea mosaic virus can be stably modeled as assemblies of independent ELNEDIN models, and that ELNEDIN models show significant promise for modeling protein-protein association processes.
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Affiliation(s)
- Xavier Periole
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco Cavalli
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Siewert-Jan Marrink
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Marco A Ceruso
- Department of Chemistry and Biochemistry and Institute for Macromolecular Assemblies, The City College of New York, 160 Convent Ave, New York, New York 10031, and Groningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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49
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50
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Candel AM, Cobos ES, Conejero-Lara F, Martinez JC. Evaluation of folding co-operativity of a chimeric protein based on the molecular recognition between polyproline ligands and SH3 domains. Protein Eng Des Sel 2009; 22:597-606. [PMID: 19617233 DOI: 10.1093/protein/gzp041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In previous work, we designed a chimeric protein, named SPCp41, to evaluate the thermodynamics of the interaction between SH3 domains and proline-rich ligands by combining thermal unfolding measurements and mutagenesis. Here, we have investigated the energetic integrity of the chain extension corresponding to the ligand sequence into the native structure, since the opposite will produce changes in the folding mechanism of the SH3 domain that may give rise to undesirable contributions to the thermodynamic parameters. We have analysed the folding-unfolding kinetics under standard conditions (50 mM phosphate pH 7). Kinetic evolutions are well described by a bi-exponential where, on top of the main kinetic phase, a low-populated slower phase appears as a consequence of cis-trans isomerisation of Pro39, as demonstrated by the influence of prolyl isomerases and by mutational analysis. There is also a burst phase possibly due to a productive formation of some helical ensembles. The main evolution, accounting for the true folding kinetics of SPCp41, can be considered as a two-state process, where the folding transition state produces essentially the same picture shown by the circular permutant S19-P20s (the 'nucleus' of the design) and the ligand will dock at the latter stages of the two-state process. Thus, all conclusions argue in favour of the effectiveness of SPCp41 to study energetic, dynamic and structural aspects of SH3-ligand interactions.
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Affiliation(s)
- Adela M Candel
- Departamento de Quimica Fisica e Instituto de Biotecnologia, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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