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Fersht AR. From covalent transition states in chemistry to noncovalent in biology: from β- to Φ-value analysis of protein folding. Q Rev Biophys 2024; 57:e4. [PMID: 38597675 DOI: 10.1017/s0033583523000045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Solving the mechanism of a chemical reaction requires determining the structures of all the ground states on the pathway and the elusive transition states linking them. 2024 is the centenary of Brønsted's landmark paper that introduced the β-value and structure-activity studies as the only experimental means to infer the structures of transition states. It involves making systematic small changes in the covalent structure of the reactants and analysing changes in activation and equilibrium-free energies. Protein engineering was introduced for an analogous procedure, Φ-value analysis, to analyse the noncovalent interactions in proteins central to biological chemistry. The methodology was developed first by analysing noncovalent interactions in transition states in enzyme catalysis. The mature procedure was then applied to study transition states in the pathway of protein folding - 'part (b) of the protein folding problem'. This review describes the development of Φ-value analysis of transition states and compares and contrasts the interpretation of β- and Φ-values and their limitations. Φ-analysis afforded the first description of transition states in protein folding at the level of individual residues. It revealed the nucleation-condensation folding mechanism of protein domains with the transition state as an expanded, distorted native structure, containing little fully formed secondary structure but many weak tertiary interactions. A spectrum of transition states with various degrees of structural polarisation was then uncovered that spanned from nucleation-condensation to the framework mechanism of fully formed secondary structure. Φ-analysis revealed how movement of the expanded transition state on an energy landscape accommodates the transition from framework to nucleation-condensation mechanisms with a malleability of structure as a unifying feature of folding mechanisms. Such movement follows the rubric of analysis of classical covalent chemical mechanisms that began with Brønsted. Φ-values are used to benchmark computer simulation, and Φ and simulation combine to describe folding pathways at atomic resolution.
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Affiliation(s)
- Alan R Fersht
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Gonville and Caius College, University of Cambridge, Cambridge, UK
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Xiong J, Gao M, Zhou J, Liu S, Su Z, Liu Z, Huang Y. The influence of intrinsic folding mechanism of an unfolded protein on the coupled folding-binding process during target recognition. Proteins 2018; 87:265-275. [PMID: 30520528 DOI: 10.1002/prot.25646] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Revised: 09/28/2018] [Accepted: 11/29/2018] [Indexed: 11/11/2022]
Abstract
Intrinsically disordered proteins (IDPs) are extensively involved in dynamic signaling processes which require a high association rate and a high dissociation rate for rapid binding/unbinding events and at the same time a sufficient high affinity for specific recognition. Although the coupled folding-binding processes of IDPs have been extensively studied, it is still impossible to predict whether an unfolded protein is suitable for molecular signaling via coupled folding-binding. In this work, we studied the interplay between intrinsic folding mechanisms and coupled folding-binding process for unfolded proteins through molecular dynamics simulations. We first studied the folding process of three representative IDPs with different folded structures, that is, c-Myb, AF9, and E3 rRNase. We found the folding free energy landscapes of IDPs are downhill or show low barriers. To further study the influence of intrinsic folding mechanism on the binding process, we modulated the folding mechanism of barnase via circular permutation and simulated the coupled folding-binding process between unfolded barnase permutant and folded barstar. Although folding of barnase was coupled to target binding, the binding kinetics was significantly affected by the intrinsic folding free energy barrier, where reducing the folding free energy barrier enhances binding rate up to two orders of magnitude. This accelerating effect is different from previous results which reflect the effect of structure flexibility on binding kinetics. Our results suggest that coupling the folding of an unfolded protein with no/low folding free energy barrier with its target binding may provide a way to achieve high specificity and rapid binding/unbinding kinetics simultaneously.
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Affiliation(s)
- Junwen Xiong
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Meng Gao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Jingjing Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Sen Liu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhengding Su
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
| | - Zhirong Liu
- College of Chemistry and Molecular Engineering, and Beijing National Laboratory for Molecular Sciences (BNLMS), Peking University, Beijing, China
| | - Yongqi Huang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Hubei University of Technology, Wuhan, China.,Hubei University of Technology, Institute of Biomedical and Pharmaceutical Sciences, Key Laboratory of Industrial Fermentation (Ministry of Education), Wuhan, China
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Yue Z, Shen J. pH-Dependent cooperativity and existence of a dry molten globule in the folding of a miniprotein BBL. Phys Chem Chem Phys 2018; 20:3523-3530. [PMID: 29336449 DOI: 10.1039/c7cp08296g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Solution pH plays an important role in protein dynamics, stability, and folding; however, detailed mechanisms remain poorly understood. Here we use continuous constant pH molecular dynamics in explicit solvent with pH replica exchange to describe the pH profile of the folding cooperativity of a miniprotein BBL, which has drawn intense debate in the past. Our data reconciled the two opposing hypotheses (downhill vs. two-state) and uncovered a sparsely populated unfolding intermediate. As pH is lowered from 7 to 5, the folding barrier vanishes. As pH continues to decrease, the unfolding barrier lowers and denaturation is triggered by the protonation of Asp162, consistent with experimental evidence. Interestingly, unfolding proceeded via an intermediate, with intact secondary structure and a compact, unlocked hydrophobic core shielded from solvent, lending support to the recent hypothesis of a universal dry molten globule in protein folding. Our work demonstrates that constant pH molecular dynamics is a unique tool for testing this and other hypotheses to advance the knowledge in protein dynamics, stability, and folding.
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Affiliation(s)
- Zhi Yue
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, MD 21201-1075, USA.
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Borgohain G, Mandal B, Paul S. Molecular dynamics approach to understand the denaturing effect of a millimolar concentration of dodine on a λ-repressor and counteraction by trehalose. Phys Chem Chem Phys 2017; 19:13160-13171. [DOI: 10.1039/c6cp08289k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Here, we use a molecular dynamics approach to calculate the spatial distribution function of the ternary water–dodine–trehalose (1.0 M) system.
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Affiliation(s)
- Gargi Borgohain
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
| | | | - Sandip Paul
- Department of Chemistry
- Indian Institute of Technology
- Guwahati
- India
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5
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Abstract
Markov state models (MSMs) are an extremely useful tool for understanding the conformational dynamics of macromolecules and for analyzing MD simulations in a quantitative fashion. They have been extensively used for peptide and protein folding, for small molecule binding, and for the study of native ensemble dynamics. Here, we adapt the MSM methodology to gain insight into the dynamics of misfolded states. To overcome possible flaws in root-mean-square deviation (RMSD)-based metrics, we introduce a novel discretization approach, based on coarse-grained contact maps. In addition, we extend the MSM methodology to include "sink" states in order to account for the irreversibility (on simulation time scales) of processes like protein misfolding. We apply this method to analyze the mechanism of misfolding of tandem repeats of titin domains, and how it is influenced by confinement in a chaperonin-like cavity.
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Affiliation(s)
- Anshul Sirur
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - David De Sancho
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
| | - Robert B Best
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW Cambridge, United Kingdom
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de Sancho D, Best RB. Reconciling Intermediates in Mechanical Unfolding Experiments with Two-State Protein Folding in Bulk. J Phys Chem Lett 2016; 7:3798-3803. [PMID: 27626458 PMCID: PMC5597958 DOI: 10.1021/acs.jpclett.6b01722] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Most experimentally well-characterized single domain proteins of less than 100 residues have been found to be two-state folders. That is, only two distinct populations can explain both equilibrium and kinetic measurements. Results from single molecule force spectroscopy, where a protein is unfolded by applying a mechanical pulling force to its ends, have largely confirmed this description for proteins found to be two-state in ensemble experiments. Recently, however, stable intermediates have been reported in mechanical unfolding experiments on a cold-shock protein previously found to be a prototypical two-state folder. Here, we tackle this discrepancy using free energy landscapes and Markov state models derived from coarse-grained molecular simulations. We show that protein folding intermediates can be selectively stabilized by the pulling force and that the populations of these intermediates vary in a force-dependent manner. Our model qualitatively captures the experimental results and suggests a possible origin of the apparent discrepancy.
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Affiliation(s)
| | - Robert B Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , Bethesda, Maryland 20892-0520, United States
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Naganathan AN, De Sancho D. Bridging Experiments and Native-Centric Simulations of a Downhill Folding Protein. J Phys Chem B 2015; 119:14925-33. [DOI: 10.1021/acs.jpcb.5b09568] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - David De Sancho
- CIC nanoGUNE, Tolosa Hiribidea,
76, E-20018 Donostia-San
Sebastián, Spain
- IKERBASQUE, Basque Foundation for Science, María Díaz de Haro 3, 48013 Bilbao, Spain
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Zheng W, De Sancho D, Hoppe T, Best RB. Dependence of internal friction on folding mechanism. J Am Chem Soc 2015; 137:3283-90. [PMID: 25721133 PMCID: PMC4379956 DOI: 10.1021/ja511609u] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Indexed: 12/25/2022]
Abstract
An outstanding challenge in protein folding is understanding the origin of "internal friction" in folding dynamics, experimentally identified from the dependence of folding rates on solvent viscosity. A possible origin suggested by simulation is the crossing of local torsion barriers. However, it was unclear why internal friction varied from protein to protein or for different folding barriers of the same protein. Using all-atom simulations with variable solvent viscosity, in conjunction with transition-path sampling to obtain reaction rates and analysis via Markov state models, we are able to determine the internal friction in the folding of several peptides and miniproteins. In agreement with experiment, we find that the folding events with greatest internal friction are those that mainly involve helix formation, while hairpin formation exhibits little or no evidence of friction. Via a careful analysis of folding transition paths, we show that internal friction arises when torsion angle changes are an important part of the folding mechanism near the folding free energy barrier. These results suggest an explanation for the variation of internal friction effects from protein to protein and across the energy landscape of the same protein.
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Affiliation(s)
- Wenwei Zheng
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - David De Sancho
- Department
of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- CIC
nanoGUNE, 20018 Donostia−San Sebastián, Spain
- IKERBASQUE,
Basque Foundation for Science, Maria Diaz de Haro 3, 48013 Bilbao, Spain
| | - Travis Hoppe
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
| | - Robert B. Best
- Laboratory
of Chemical Physics, National Institute of Diabetes and Digestive
and Kidney Diseases, National Institutes
of Health, Bethesda, Maryland 20892, United
States
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