1
|
da Silva FB, Martins de Oliveira V, de Oliveira Junior AB, Contessoto VDG, Leite VBP. Probing the Energy Landscape of Spectrin R15 and R16 and the Effects of Non-native Interactions. J Phys Chem B 2023; 127:1291-1300. [PMID: 36723393 DOI: 10.1021/acs.jpcb.2c06178] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding the details of a protein folding mechanism can be a challenging and complex task. One system with an interesting folding behavior is the α-spectrin domain, where the R15 folds three-orders of magnitude faster than its homologues R16 and R17, despite having similar structures. The molecular origins that explain these folding rate differences remain unclear, but our previous work revealed that a combined effect produced by non-native interactions could be a reasonable cause for these differences. In this study, we explore further the folding process by identifying the molecular paths, metastable states, and the collective motions that lead these unfolded proteins to their native state conformation. Our results uncovered the differences between the folding pathways for the wild-type R15 and R16 and an R16 mutant. The metastable ensembles that speed down the folding were identified using an energy landscape visualization method (ELViM). These ensembles correspond to similar experimentally reported configurations. Our observations indicate that the non-native interactions are also associated with secondary structure misdocking. This computational methodology can be used as a fast, straightforward protocol for shedding light on systems with unclear folding or conformational traps.
Collapse
Affiliation(s)
- Fernando Bruno da Silva
- Department of Physics, São Paulo State University (UNESP), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, São Paulo15054-000, Brazil
| | - Vinícius Martins de Oliveira
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland21201, United States
| | | | | | - 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 Paulo15054-000, Brazil
| |
Collapse
|
2
|
Xia C, Kang W, Wang J, Wang W. Temperature Dependence of Internal Friction of Peptides. J Phys Chem B 2021; 125:2821-2832. [PMID: 33689339 DOI: 10.1021/acs.jpcb.0c09056] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Internal friction is a valuable concept to describe the kinetics of proteins. As is well known, internal friction can be modulated by solvent features (such as viscosity). How can internal friction be affected by environmental temperature? The answer to this question is not evident. In the present work, we approach this problem with simulations on two model peptides. The thermodynamics and relaxation kinetics are characterized through long molecular dynamics simulations, with the viscosity modulated by varying the mass of solvent molecules. Based on the extrapolation to zero viscosity together with scaling of the relaxation time scales, we discover that internal friction is almost invariant at various temperatures. Controlled simulations further support the idea that internal friction is independent of environmental temperature. Comparisons between the two model peptides help us to understand the diverse phenomena in experiments.
Collapse
Affiliation(s)
- Chenliang Xia
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wenbin Kang
- School of Public Health and Management, Hubei University of Medicine, Shiyan 442000, P.R. China
| | - Jun Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| | - Wei Wang
- School of Physics, Nanjing University, Nanjing 210093, P.R.China.,National Laboratory of Solid State Microstructure, Collaborative Innovation Center of Advanced Microstructures, Nanjing 210093, P.R.China
| |
Collapse
|
3
|
Ruiz-Ortiz I, De Sancho D. Competitive binding of HIF-1α and CITED2 to the TAZ1 domain of CBP from molecular simulations. Phys Chem Chem Phys 2020; 22:8118-8127. [DOI: 10.1039/d0cp00328j] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Many intrinsically disordered proteins (IDPs) are involved in complex signalling networks inside the cell.
Collapse
Affiliation(s)
- Irene Ruiz-Ortiz
- Donostia International Physics Center
- Donostia-San Sebastián
- Spain
| | - David De Sancho
- Donostia International Physics Center
- Donostia-San Sebastián
- Spain
- University of the Basque Country
- Faculty of Chemistry
| |
Collapse
|
4
|
Bruno da Silva F, Contessoto VG, de Oliveira VM, Clarke J, Leite VBP. Non-Native Cooperative Interactions Modulate Protein Folding Rates. J Phys Chem B 2018; 122:10817-10824. [DOI: 10.1021/acs.jpcb.8b08990] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Fernando Bruno da Silva
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| | - Vinícius G. Contessoto
- Brazilian Bioethanol Science and Technology Laboratory - CTBE, Campinas - São Paulo 13083-100, Brazil
| | - Vinícius M. de Oliveira
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| | - Jane Clarke
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Vitor B. P. Leite
- Department of Physics, Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José do Rio Preto - São Paulo 15054-000, Brazil
| |
Collapse
|
5
|
Yrazu FM, Pinamonti G, Clementi C. The Effect of Electrostatic Interactions on the Folding Kinetics of a 3-α-Helical Bundle Protein Family. J Phys Chem B 2018; 122:11800-11806. [PMID: 30277393 DOI: 10.1021/acs.jpcb.8b08676] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The trio of protein segment repeats called spectrins diverges by more than 2 orders of magnitude in their folding and unfolding rates, despite having very similar stabilities and almost coincidental topologies. Experimental studies revealed that the mutation of five particular residues dramatically alters the kinetic rates in the slow folders, making them similar to the rates of the fast folder. This is considered to be an exceptional behavior which seems in principle to challenge the current understanding of the protein folding process. In this work, we analyze this scenario, using a simplified computational model, combined with state-of-the-art kinetic analysis techniques. Our model faithfully separates the kinetics of the fast and slow folders and captures the effect of the five mutations. We show that the inclusion of electrostatics in the model is necessary to explain the experimental findings.
Collapse
Affiliation(s)
- Fernando Miguel Yrazu
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States
| | - Giovanni Pinamonti
- Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany
| | - Cecilia Clementi
- Department of Chemical and Biomolecular Engineering , Rice University , Houston , Texas 77005 , United States.,Department of Informatics and Mathematics , Freie Universität Berlin , 14195 Berlin , Germany.,Center for Theoretical Biological Physics and Department of Chemistry , Rice University , Houston , Texas 77005 , United States
| |
Collapse
|
6
|
Comparative mechanical unfolding studies of spectrin domains R15, R16 and R17. J Struct Biol 2017; 201:162-170. [PMID: 29221897 DOI: 10.1016/j.jsb.2017.12.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 11/08/2017] [Accepted: 12/04/2017] [Indexed: 11/20/2022]
Abstract
Spectrins belong to repetitive three-helix bundle proteins that have vital functions in multicellular organisms and are of potential value in nanotechnology. To reveal the unique physical features of repeat proteins we have studied the structural and mechanical properties of three repeats of chicken brain α-spectrin (R15, R16 and R17) at the atomic level under stretching at constant velocities (0.01, 0.05 and 0.1 Å·ps-1) and constant forces (700 and 900 pN) using molecular dynamics (MD) simulations at T = 300 K. 114 independent MD simulations were performed and their analysis has been done. Despite structural similarity of these domains we have found that R15 is less mechanically stable than R16, which is less stable than R17. This result is in agreement with the thermal unfolding rates. Moreover, we have observed the relationship between mechanical stability, flexibility of the domains and the number of aromatic residues involved in aromatic clusters.
Collapse
|
7
|
Tian P, Best RB. Structural Determinants of Misfolding in Multidomain Proteins. PLoS Comput Biol 2016; 12:e1004933. [PMID: 27163669 PMCID: PMC4862688 DOI: 10.1371/journal.pcbi.1004933] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/21/2016] [Indexed: 12/02/2022] Open
Abstract
Recent single molecule experiments, using either atomic force microscopy (AFM) or Förster resonance energy transfer (FRET) have shown that multidomain proteins containing tandem repeats may form stable misfolded structures. Topology-based simulation models have been used successfully to generate models for these structures with domain-swapped features, fully consistent with the available data. However, it is also known that some multidomain protein folds exhibit no evidence for misfolding, even when adjacent domains have identical sequences. Here we pose the question: what factors influence the propensity of a given fold to undergo domain-swapped misfolding? Using a coarse-grained simulation model, we can reproduce the known propensities of multidomain proteins to form domain-swapped misfolds, where data is available. Contrary to what might be naively expected based on the previously described misfolding mechanism, we find that the extent of misfolding is not determined by the relative folding rates or barrier heights for forming the domains present in the initial intermediates leading to folded or misfolded structures. Instead, it appears that the propensity is more closely related to the relative stability of the domains present in folded and misfolded intermediates. We show that these findings can be rationalized if the folded and misfolded domains are part of the same folding funnel, with commitment to one structure or the other occurring only at a relatively late stage of folding. Nonetheless, the results are still fully consistent with the kinetic models previously proposed to explain misfolding, with a specific interpretation of the observed rate coefficients. Finally, we investigate the relation between interdomain linker length and misfolding, and propose a simple alchemical model to predict the propensity for domain-swapped misfolding of multidomain proteins.
Collapse
Affiliation(s)
- Pengfei Tian
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| |
Collapse
|
8
|
Panneerselvam S, Durai P, Yesudhas D, Achek A, Kwon HK, Choi S. Cysteine redox state plays a key role in the inter-domain movements of HMGB1: a molecular dynamics simulation study. RSC Adv 2016. [DOI: 10.1039/c6ra16343b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We have modelled and simulated different states of HMGB1, suggesting that the fully reduced HMGB1 maintains the inter-domain movements during the activity.
Collapse
Affiliation(s)
| | | | - Dhanusha Yesudhas
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Asma Achek
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Hyuk-Kwon Kwon
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| | - Sangdun Choi
- Department of Molecular Science and Technology
- Ajou University
- Suwon 443-749
- Korea
| |
Collapse
|
9
|
Chen T, Chan HS. Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins. PLoS Comput Biol 2015; 11:e1004260. [PMID: 26016652 PMCID: PMC4446218 DOI: 10.1371/journal.pcbi.1004260] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 03/29/2015] [Indexed: 11/18/2022] Open
Abstract
The bacterial colicin-immunity proteins Im7 and Im9 fold by different mechanisms. Experimentally, at pH 7.0 and 10°C, Im7 folds in a three-state manner via an intermediate but Im9 folding is two-state-like. Accordingly, Im7 exhibits a chevron rollover, whereas the chevron arm for Im9 folding is linear. Here we address the biophysical basis of their different behaviors by using native-centric models with and without additional transferrable, sequence-dependent energies. The Im7 chevron rollover is not captured by either a pure native-centric model or a model augmented by nonnative hydrophobic interactions with a uniform strength irrespective of residue type. By contrast, a more realistic nonnative interaction scheme that accounts for the difference in hydrophobicity among residues leads simultaneously to a chevron rollover for Im7 and an essentially linear folding chevron arm for Im9. Hydrophobic residues identified by published experiments to be involved in nonnative interactions during Im7 folding are found to participate in the strongest nonnative contacts in this model. Thus our observations support the experimental perspective that the Im7 folding intermediate is largely underpinned by nonnative interactions involving large hydrophobics. Our simulation suggests further that nonnative effects in Im7 are facilitated by a lower local native contact density relative to that of Im9. In a one-dimensional diffusion picture of Im7 folding with a coordinate- and stability-dependent diffusion coefficient, a significant chevron rollover is consistent with a diffusion coefficient that depends strongly on native stability at the conformational position of the folding intermediate. In order to fold correctly, a globular protein must avoid being trapped in wrong, i.e., nonnative conformations. Thus a biophysical account of how attractive nonnative interactions are bypassed by some amino acid sequences but not others is key to deciphering protein structure and function. We examine two closely related bacterial immunity proteins, Im7 and Im9, that are experimentally known to fold very differently: Whereas Im9 folds directly, Im7 folds through a mispacked conformational intermediate. A simple model we developed accounts for their intriguingly different folding kinetics in terms of a balance between the density of native-promoting contacts and the hydrophobicity of local amino acid sequences. This emergent principle is extensible to other biomolecular recognition processes.
Collapse
Affiliation(s)
- Tao Chen
- Departments of Biochemistry, of Molecular Genetics, and of Physics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Hue Sun Chan
- Departments of Biochemistry, of Molecular Genetics, and of Physics, University of Toronto, Toronto, Ontario M5S 1A8, Canada
- * E-mail:
| |
Collapse
|
10
|
Yadahalli S, Hemanth Giri Rao VV, Gosavi S. Modeling Non-Native Interactions in Designed Proteins. Isr J Chem 2014. [DOI: 10.1002/ijch.201400035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
11
|
Galzitskaya OV, Pereyaslavets LB, Glyakina AV. Folding of Right- and Left-Handed Three-Helix Proteins. Isr J Chem 2014. [DOI: 10.1002/ijch.201300146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
12
|
Chen T, Chan HS. Effects of desolvation barriers and sidechains on local–nonlocal coupling and chevron behaviors in coarse-grained models of protein folding. Phys Chem Chem Phys 2014; 16:6460-79. [DOI: 10.1039/c3cp54866j] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Coarse-grained protein chain models with desolvation barriers or sidechains lead to stronger local–nonlocal coupling and more linear chevron plots.
Collapse
Affiliation(s)
- Tao Chen
- Departments of Biochemistry
- of Molecular Genetics
- of Physics
- University of Toronto
- Toronto, Canada
| | - Hue Sun Chan
- Departments of Biochemistry
- of Molecular Genetics
- of Physics
- University of Toronto
- Toronto, Canada
| |
Collapse
|
13
|
Markiewicz BN, Jo H, Culik RM, DeGrado WF, Gai F. Assessment of local friction in protein folding dynamics using a helix cross-linker. J Phys Chem B 2013; 117:14688-96. [PMID: 24205975 DOI: 10.1021/jp409334h] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Internal friction arising from local steric hindrance and/or the excluded volume effect plays an important role in controlling not only the dynamics of protein folding but also conformational transitions occurring within the native state potential well. However, experimental assessment of such local friction is difficult because it does not manifest itself as an independent experimental observable. Herein, we demonstrate, using the miniprotein trp-cage as a testbed, that it is possible to selectively increase the local mass density in a protein and hence the magnitude of local friction, thus making its effect directly measurable via folding kinetic studies. Specifically, we show that when a helix cross-linker, m-xylene, is placed near the most congested region of the trp-cage it leads to a significant decrease in both the folding rate (by a factor of 3.8) and unfolding rate (by a factor of 2.5 at 35 °C) but has little effect on protein stability. Thus, these results, in conjunction with those obtained with another cross-linked trp-cage and two uncross-linked variants, demonstrate the feasibility of using a nonperturbing cross-linker to help quantify the effect of internal friction. In addition, we estimate that a m-xylene cross-linker could lead to an increase in the roughness of the folding energy landscape by as much as 0.4-1.0k(B)T.
Collapse
Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and §Department of Biochemistry & Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | | | | | | | | |
Collapse
|
14
|
Carter JW, Baker CM, Best RB, De Sancho D. Engineering folding dynamics from two-state to downhill: application to λ-repressor. J Phys Chem B 2013; 117:13435-43. [PMID: 24079652 PMCID: PMC3840902 DOI: 10.1021/jp405904g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
One
strategy for reaching the downhill folding regime, primarily
exploited for the λ6–85 protein fragment,
consists of cumulatively introducing mutations that speed up folding.
This is an experimentally demanding process where chemical intuition
usually serves as a guide for the choice of amino acid residues to
mutate. Such an approach can be aided by computational methods that
screen for protein engineering hot spots. Here we present one such
method that involves sampling the energy landscape of the pseudo-wild-type
protein and investigating the effect of point mutations on this landscape.
Using a novel metric for the cooperativity, we identify those residues
leading to the least cooperative folding. The folding dynamics of
the selected mutants are then directly characterized and the differences
in the kinetics are analyzed within a Markov-state model framework.
Although the method is general, here we present results for a coarse-grained
topology-based simulation model of λ-repressor, whose barrier
is reduced from an initial value of ∼4kBT at the midpoint to ∼1kBT, thereby reaching the downhill folding
regime.
Collapse
Affiliation(s)
- James W Carter
- Department of Chemistry, University of Cambridge , Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | | | | | | |
Collapse
|