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Wang D, Frechette LB, Best RB. On the role of native contact cooperativity in protein folding. Proc Natl Acad Sci U S A 2024; 121:e2319249121. [PMID: 38776371 PMCID: PMC11145220 DOI: 10.1073/pnas.2319249121] [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: 11/02/2023] [Accepted: 04/11/2024] [Indexed: 05/25/2024] Open
Abstract
The consistency of energy landscape theory predictions with available experimental data, as well as direct evidence from molecular simulations, have shown that protein folding mechanisms are largely determined by the contacts present in the native structure. As expected, native contacts are generally energetically favorable. However, there are usually at least as many energetically favorable nonnative pairs owing to the greater number of possible nonnative interactions. This apparent frustration must therefore be reduced by the greater cooperativity of native interactions. In this work, we analyze the statistics of contacts in the unbiased all-atom folding trajectories obtained by Shaw and coworkers, focusing on the unfolded state. By computing mutual cooperativities between contacts formed in the unfolded state, we show that native contacts form the most cooperative pairs, while cooperativities among nonnative or between native and nonnative contacts are typically much less favorable or even anticooperative. Furthermore, we show that the largest network of cooperative interactions observed in the unfolded state consists mainly of native contacts, suggesting that this set of mutually reinforcing interactions has evolved to stabilize the native state.
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Affiliation(s)
- David Wang
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
- Department of Biology, Johns Hopkins University, Baltimore, MD21218
| | - Layne B. Frechette
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
- Martin A. Fisher School of Physics, Brandeis University, Waltham, MA02453
| | - Robert B. Best
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD20892-0520
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Patel A, Tiwari K, Asrani P, Alothaid H, Alahmari AFA, Mirdad R, Ajmal MR, Tarique M. Glutaredoxin proteins from E. coli isoforms were compared in terms of energy frustration. BRAZ J BIOL 2023; 83:e273091. [PMID: 37729314 DOI: 10.1590/1519-6984.273091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/05/2023] [Indexed: 09/22/2023] Open
Abstract
Glutaredoxin (GRXs) protein plays a vital role inside the cell, including redox control of transcription to the cell's antioxidant defense, apoptosis, and cellular differentiation regulation. In this study, we have investigated the energy landscape and characterized the pattern of local frustration in different forms and states of the GRX protein ofE. coli.Analysis was done on the conformational alterations, significant changes in the frustration pattern, and different GRXs such as GRX-II, GRX-III, GRX-II-GSH, and GRX-III-GSH complex. We have found the practice of frustration, and structure was quite similar in the same isoform having different states of protein; however, a significant difference was observed between different isoforms. Moreover, oxidation of GRX-I introduced an extra α-helix increasing the destabilizing interactions within the protein. The study of frustrated contacts on oxidized and reduced GRX and with bound and unbound Glutathione indicates its potential application in activating and regulating the behavior of GRXs.
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Affiliation(s)
- A Patel
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Kingdom of Saudi Arabia
| | - K Tiwari
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Kingdom of Saudi Arabia
- Amity University, Amity Institute of Microbial Biotechnology, Noida, UP, India
| | - P Asrani
- Amity University, Amity Institute of Microbial Biotechnology, Noida, UP, India
| | - H Alothaid
- Al Baha University, Faculty of Applied Medical Sciences, Department of Basic Medical Sciences, Al Baha, Al Baha Province, Saudi Arabia
| | - A F A Alahmari
- King Khalid University, College of Medicine, Department of Clinical Biochemistry, Abha, Saudi Arabia
| | - R Mirdad
- King Khalid University, Department of Surgery, Abha, Saudi Arabia
| | - M R Ajmal
- University of Tabuk, Faculty of Science, Biochemistry Department, Physical Biochemistry Research Laboratory, Tabuk, Saudi Arabia
| | - M Tarique
- Almanac Life Science India Private Limited, New Delhi, India
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Observation of Continuous Contraction and a Metastable Misfolded State during the Collapse and Folding of a Small Protein. J Mol Biol 2019; 431:3814-3826. [DOI: 10.1016/j.jmb.2019.07.024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/12/2019] [Accepted: 07/12/2019] [Indexed: 01/22/2023]
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Cinar H, Fetahaj Z, Cinar S, Vernon RM, Chan HS, Winter RHA. Temperature, Hydrostatic Pressure, and Osmolyte Effects on Liquid-Liquid Phase Separation in Protein Condensates: Physical Chemistry and Biological Implications. Chemistry 2019; 25:13049-13069. [PMID: 31237369 DOI: 10.1002/chem.201902210] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 06/23/2019] [Indexed: 01/04/2023]
Abstract
Liquid-liquid phase separation (LLPS) of proteins and other biomolecules play a critical role in the organization of extracellular materials and membrane-less compartmentalization of intra-organismal spaces through the formation of condensates. Structural properties of such mesoscopic droplet-like states were studied by spectroscopy, microscopy, and other biophysical techniques. The temperature dependence of biomolecular LLPS has been studied extensively, indicating that phase-separated condensed states of proteins can be stabilized or destabilized by increasing temperature. In contrast, the physical and biological significance of hydrostatic pressure on LLPS is less appreciated. Summarized here are recent investigations of protein LLPS under pressures up to the kbar-regime. Strikingly, for the cases studied thus far, LLPSs of both globular proteins and intrinsically disordered proteins/regions are typically more sensitive to pressure than the folding of proteins, suggesting that organisms inhabiting the deep sea and sub-seafloor sediments, under pressures up to 1 kbar and beyond, have to mitigate this pressure-sensitivity to avoid unwanted destabilization of their functional biomolecular condensates. Interestingly, we found that trimethylamine-N-oxide (TMAO), an osmolyte upregulated in deep-sea fish, can significantly stabilize protein droplets under pressure, pointing to another adaptive advantage for increased TMAO concentrations in deep-sea organisms besides the osmolyte's stabilizing effect against protein unfolding. As life on Earth might have originated in the deep sea, pressure-dependent LLPS is pertinent to questions regarding prebiotic proto-cells. Herein, we offer a conceptual framework for rationalizing the recent experimental findings and present an outline of the basic thermodynamics of temperature-, pressure-, and osmolyte-dependent LLPS as well as a molecular-level statistical mechanics picture in terms of solvent-mediated interactions and void volumes.
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Affiliation(s)
- Hasan Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Zamira Fetahaj
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Süleyman Cinar
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
| | - Robert M Vernon
- Molecular Medicine, The Hospital for Sick Children, Toronto, Ontario, M5G 0A4, Canada
| | - Hue Sun Chan
- Department of Biochemistry, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada.,Department of Molecular Genetics, Faculty of Medicine, University of Toronto, Ontario, M5S 1A8, Canada
| | - Roland H A Winter
- Physical Chemistry I-Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, Otto-Hahn Strasse 4a, 44227, Dortmund, Germany
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5
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Cinar S, Cinar H, Chan HS, Winter R. Pressure-Sensitive and Osmolyte-Modulated Liquid–Liquid Phase Separation of Eye-Lens γ-Crystallins. J Am Chem Soc 2019; 141:7347-7354. [DOI: 10.1021/jacs.8b13636] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Süleyman Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hasan Cinar
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
| | - Hue Sun Chan
- Departments of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Toronto, Toronto, Ontario M5S 1A8, Canada
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund, Otto-Hahn-Strasse 4a, 44227 Dortmund, Germany
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Cheng C, Wu J, Liu G, Shi S, Chen T. Effects of Non-native Interactions on Frustrated Proteins Folding under Confinement. J Phys Chem B 2018; 122:7654-7667. [DOI: 10.1021/acs.jpcb.8b04147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Chenqian Cheng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Gaoyuan Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Suqing Shi
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi’an 710127, P. R. China
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