1
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Zhang Z, Cai Y, Zheng N, Deng Y, Gao L, Wang Q, Xia X. Diverse models of cavity engineering in enzyme modification: Creation, filling, and reshaping. Biotechnol Adv 2024; 72:108346. [PMID: 38518963 DOI: 10.1016/j.biotechadv.2024.108346] [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] [Received: 09/08/2023] [Revised: 03/07/2024] [Accepted: 03/19/2024] [Indexed: 03/24/2024]
Abstract
Most enzyme modification strategies focus on designing the active sites or their surrounding structures. Interestingly, a large portion of the enzymes (60%) feature active sites located within spacious cavities. Despite recent discoveries, cavity-mediated enzyme engineering remains crucial for enhancing enzyme properties and unraveling folding-unfolding mechanisms. Cavity engineering influences enzyme stability, catalytic activity, specificity, substrate recognition, and docking. This article provides a comprehensive review of various cavity engineering models for enzyme modification, including cavity creation, filling, and reshaping. Additionally, it also discusses feasible tools for geometric analysis, functional assessment, and modification of cavities, and explores potential future research directions in this field. Furthermore, a promising universal modification strategy for cavity engineering that leverages state-of-the-art technologies and methodologies to tailor cavities according to the specific requirements of industrial production conditions is proposed.
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Affiliation(s)
- Zehua Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yongchao Cai
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Nan Zheng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Yu Deng
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Ling Gao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Qiong Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China.
| | - Xiaole Xia
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, PR China; College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin 300457, PR China.
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2
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Byrne PO, McLellan JS. Principles and practical applications of structure-based vaccine design. Curr Opin Immunol 2022; 77:102209. [PMID: 35598506 PMCID: PMC9611442 DOI: 10.1016/j.coi.2022.102209] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 04/12/2022] [Accepted: 04/15/2022] [Indexed: 12/16/2022]
Abstract
Viral proteins fold into a variety of
structures as they perform their functions. Structure-based vaccine
design aims to exploit knowledge of an antigen’s architecture to
stabilize it in a vulnerable conformation. We summarize the general
principles of structure-based vaccine design, with a focus on the major
types of sequence modifications: proline, disulfide, cavity-filling,
electrostatic and hydrogen-bond substitution, as well as domain deletion.
We then review recent applications of these principles to vaccine-design
efforts across five viral families: Coronaviridae,
Orthomyxoviridae, Paramyxoviridae, Pneumoviridae, and
Filoviridae. Outstanding challenges include
continued application of proven design principles to pathogens of
interest, as well as development of new strategies for those pathogens
that resist traditional techniques.
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3
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Naganathan AN, Kannan A. A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures. Curr Res Struct Biol 2021; 3:257-267. [PMID: 34704074 PMCID: PMC8526763 DOI: 10.1016/j.crstbi.2021.09.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 09/08/2021] [Accepted: 09/30/2021] [Indexed: 12/22/2022] Open
Abstract
Protein sequences and structures evolve by satisfying varied physical and biochemical constraints. This multi-level selection is enabled not just by the patterning of amino acids on the sequence, but also via coupling between residues in the native structure. Here, we employ an energetically detailed statistical mechanical model with millions of microstates to extract such long-range structural correlations, i.e. thermodynamic coupling free energies, from a diverse family of protein structures. We find that despite the intricate and anisotropic distribution of coupling patterns, the majority of residues (>70%) are only marginally coupled contributing to functional motions and catalysis. Physical origins of ‘sectors’, determinants of native ensemble heterogeneity in extant, ancient and designed proteins, and the basis for allostery emerge naturally from coupling free energies. The statistical framework highlights how evolutionary selection and optimization occur at the level of global interaction network for a given protein fold impacting folding, function, and allosteric outputs. Evolution of protein structures occurs at the level of global interaction network. More than 70% of the protein residues are weakly or marginally coupled. Functional ‘sector’ regions are a manifestation of marginal coupling. Coupling indices vary across the entire proteins in extant-ancient and natural-designed pairs. The proposed methodology can be used to understand allostery and epistasis.
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Affiliation(s)
- Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
| | - Adithi Kannan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai, 600036, India
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4
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Comparative Assessment of NMR Probes for the Experimental Description of Protein Folding Pathways with High-Pressure NMR. BIOLOGY 2021; 10:biology10070656. [PMID: 34356511 PMCID: PMC8301334 DOI: 10.3390/biology10070656] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/05/2021] [Accepted: 07/09/2021] [Indexed: 11/17/2022]
Abstract
Multidimensional NMR intrinsically provides multiple probes that can be used for deciphering the folding pathways of proteins: NH amide and CαHα groups are strategically located on the backbone of the protein, while CH3 groups, on the side-chain of methylated residues, are involved in important stabilizing interactions in the hydrophobic core. Combined with high hydrostatic pressure, these observables provide a powerful tool to explore the conformational landscapes of proteins. In the present study, we made a comparative assessment of the NH, CαHα, and CH3 groups for analyzing the unfolding pathway of ∆+PHS Staphylococcal Nuclease. These probes yield a similar description of the folding pathway, with virtually identical thermodynamic parameters for the unfolding reaction, despite some notable differences. Thus, if partial unfolding begins at identical pressure for these observables (especially in the case of backbone probes) and concerns similar regions of the molecule, the residues involved in contact losses are not necessarily the same. In addition, an unexpected slight shift toward higher pressure was observed in the sequence of the scenario of unfolding with CαHα when compared to amide groups.
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5
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Gopi S, Lukose B, Naganathan AN. Diverse Native Ensembles Dictate the Differential Functional Responses of Nuclear Receptor Ligand-Binding Domains. J Phys Chem B 2021; 125:3546-3555. [PMID: 33818099 DOI: 10.1021/acs.jpcb.1c00972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Native states of folded proteins are characterized by a large ensemble of conformations whose relative populations and interconversion dynamics determine the functional output. This is more apparent in transcription factors that have evolved to be inherently sensitive to small perturbations, thus fine-tuning gene expression. To explore the extent to which such functional features are imprinted on the folding landscape of transcription factor ligand-binding domains (LBDs), we characterize paralogous LBDs of the nuclear receptor (NR) family employing an energetically detailed and ensemble-based Ising-like statistical mechanical model. We find that the native ensembles of the LBDs from glucocorticoid receptor, PPAγ, and thyroid hormone receptor display a remarkable diversity in the width of the native wells, the number and nature of partially structured states, and hence the degree of conformational order. Monte Carlo simulations employing the full state representation of the ensemble highlight that many of the functional conformations coexist in equilibrium, whose relative populations are sensitive to both temperature and the strength of ligand binding. Allosteric modulation of the degree of structure at a coregulator binding site on ligand binding is shown to arise via a redistribution of populations in the native ensembles of glucocorticoid and PPAγ LBDs. Our results illustrate how functional requirements can drive the evolution of conformationally diverse native ensembles in paralogs.
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Affiliation(s)
- Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Bincy Lukose
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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6
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Ausar SF, Zhu S, Duprez J, Cohen M, Bertrand T, Steier V, Wilson DJ, Li S, Sheung A, Brookes RH, Pedyczak A, Rak A, Andrew James D. Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity. Commun Biol 2020; 3:427. [PMID: 32759959 PMCID: PMC7406505 DOI: 10.1038/s42003-020-01153-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
The mutant gdPT R9K/E129G is a genetically detoxified variant of the pertussis toxin (PTx) and represents an attractive candidate for the development of improved pertussis vaccines. The impact of the mutations on the overall protein structure and its immunogenicity has remained elusive. Here we present the crystal structure of gdPT and show that it is nearly identical to that of PTx. Hydrogen-deuterium exchange mass spectrometry revealed dynamic changes in the catalytic domain that directly impacted NAD+ binding which was confirmed by biolayer interferometry. Distal changes in dynamics were also detected in S2-S5 subunit interactions resulting in tighter packing of B-oligomer corresponding to increased thermal stability. Finally, antigen stimulation of human whole blood, analyzed by a previously unreported mass cytometry assay, indicated broader immunogenicity of gdPT compared to pertussis toxoid. These findings establish a direct link between the conserved structure of gdPT and its ability to generate a robust immune response.
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Affiliation(s)
- Salvador F Ausar
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Shaolong Zhu
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada.,Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Jessica Duprez
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Michael Cohen
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.,Fluidigm Corporation, Markham, ON, L3R 4G5, Canada
| | - Thomas Bertrand
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - Valérie Steier
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - Derek J Wilson
- Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada
| | - Stephen Li
- Fluidigm Corporation, Markham, ON, L3R 4G5, Canada
| | - Anthony Sheung
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Roger H Brookes
- Bioprocess Research and Development, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Artur Pedyczak
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada
| | - Alexey Rak
- Research Platform, Sanofi R&D, Vitry-sur-Seine, 94400, Paris, France
| | - D Andrew James
- Analytical Sciences, Sanofi Pasteur Ltd., Toronto, ON, M2R 3T4, Canada. .,Center for Research in Mass Spectrometry, Department of Chemistry, York University, Toronto, ON, M3J 1P3, Canada.
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7
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Munshi S, Rajendran D, Ramesh S, Subramanian S, Bhattacharjee K, Kumar MR, Naganathan AN. Controlling Structure and Dimensions of a Disordered Protein via Mutations. Biochemistry 2019; 59:171-174. [PMID: 31557007 PMCID: PMC7115935 DOI: 10.1021/acs.biochem.9b00678] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The dimensions of intrinsically disordered proteins (IDPs) are sensitive to small energetic-entropic differences between intramolecular and protein–solvent interactions. This is commonly observed on modulating solvent composition and temperature. However, the inherently heterogeneous conformational landscape of IDPs is also expected to be influenced by mutations that can (de)stabilize pockets of local and even global structure, native and non-native, and hence the average dimensions. Here, we show experimental evidence for the remarkably tunable landscape of IDPs by employing the DNA-binding domain of CytR, a high-sequence-complexity IDP, as a model system. CytR exhibits a range of structure and compactness upon introducing specific mutations that modulate microscopic terms, including main-chain entropy, hydrophobicity, and electrostatics. The degree of secondary structure, as monitored by far-UV circular dichroism (CD), is strongly correlated to average ensemble dimensions for 14 different mutants of CytR and is consistent with the Uversky–Fink relation. Our experiments highlight how average ensemble dimensions can be controlled via mutations even in the disordered regime, the prevalence of non-native interactions and provide testable controls for molecular simulations.
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Affiliation(s)
- Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Divya Rajendran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Samyuktha Ramesh
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Sandhyaa Subramanian
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Kabita Bhattacharjee
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Meagha Ramana Kumar
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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8
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Munshi S, Subramanian S, Ramesh S, Golla H, Kalivarathan D, Kulkarni M, Campos LA, Sekhar A, Naganathan AN. Engineering Order and Cooperativity in a Disordered Protein. Biochemistry 2019; 58:2389-2397. [PMID: 31002232 DOI: 10.1021/acs.biochem.9b00182] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Structural disorder in proteins arises from a complex interplay between weak hydrophobicity and unfavorable electrostatic interactions. The extent to which the hydrophobic effect contributes to the unique and compact native state of proteins is, however, confounded by large compensation between multiple entropic and energetic terms. Here we show that protein structural order and cooperativity arise as emergent properties upon hydrophobic substitutions in a disordered system with non-intuitive effects on folding and function. Aided by sequence-structure analysis, equilibrium, and kinetic spectroscopic studies, we engineer two hydrophobic mutations in the disordered DNA-binding domain of CytR that act synergistically, but not in isolation, to promote structure, compactness, and stability. The double mutant, with properties of a fully ordered domain, exhibits weak cooperativity with a complex and rugged conformational landscape. The mutant, however, binds cognate DNA with an affinity only marginally higher than that of the wild type, though nontrivial differences are observed in the binding to noncognate DNA. Our work provides direct experimental evidence of the dominant role of non-additive hydrophobic effects in shaping the molecular evolution of order in disordered proteins and vice versa, which could be generalized to even folded proteins with implications for protein design and functional manipulation.
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Affiliation(s)
- Sneha Munshi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Sandhyaa Subramanian
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Samyuktha Ramesh
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Hemashree Golla
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
| | - Divakar Kalivarathan
- Department of Biotechnology , National Institute of Technology Warangal , Warangal 506004 , India
| | - Madhurima Kulkarni
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Luis A Campos
- National Biotechnology Center , Consejo Superior de Investigaciones Científicas , Darwin 3, Campus de Cantoblanco , 28049 Madrid , Spain
| | - Ashok Sekhar
- Molecular Biophysics Unit , Indian Institute of Science , Bangalore 560012 , India
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences , Indian Institute of Technology Madras , Chennai 600036 , India
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9
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Roche J, Royer CA. Lessons from pressure denaturation of proteins. J R Soc Interface 2018; 15:rsif.2018.0244. [PMID: 30282759 DOI: 10.1098/rsif.2018.0244] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 09/13/2018] [Indexed: 12/26/2022] Open
Abstract
Although it is now relatively well understood how sequence defines and impacts global protein stability in specific structural contexts, the question of how sequence modulates the configurational landscape of proteins remains to be defined. Protein configurational equilibria are generally characterized by using various chemical denaturants or by changing temperature or pH. Another thermodynamic parameter which is less often used in such studies is high hydrostatic pressure. This review discusses the basis for pressure effects on protein structure and stability, and describes how the unique mechanisms of pressure-induced unfolding can provide unique insights into protein conformational landscapes.
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Affiliation(s)
- Julien Roche
- Department of Biochemistry, Biophysics and Molecular Biology Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
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10
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Modulation of allosteric coupling by mutations: from protein dynamics and packing to altered native ensembles and function. Curr Opin Struct Biol 2018; 54:1-9. [PMID: 30268910 PMCID: PMC6420056 DOI: 10.1016/j.sbi.2018.09.004] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 08/13/2018] [Accepted: 09/10/2018] [Indexed: 01/12/2023]
Abstract
A large body of work has gone into understanding the effect of mutations on protein structure and function. Conventional treatments have involved quantifying the change in stability, activity and relaxation rates of the mutants with respect to the wild-type protein. However, it is now becoming increasingly apparent that mutational perturbations consistently modulate the packing and dynamics of a significant fraction of protein residues, even those that are located >10–15 Å from the mutated site. Such long-range modulation of protein features can distinctly tune protein stability and the native conformational ensemble contributing to allosteric modulation of function. In this review, I summarize a series of experimental and computational observations that highlight the incredibly pliable nature of proteins and their response to mutational perturbations manifested via the intra-protein interaction network. I highlight how an intimate understanding of mutational effects could pave the way for integrating stability, folding, cooperativity and even allostery within a single physical framework.
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11
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Caro JA, Wand AJ. Practical aspects of high-pressure NMR spectroscopy and its applications in protein biophysics and structural biology. Methods 2018; 148:67-80. [PMID: 29964175 PMCID: PMC6133745 DOI: 10.1016/j.ymeth.2018.06.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 01/15/2023] Open
Abstract
Pressure and temperature are the two fundamental variables of thermodynamics. Temperature and chemical perturbation are central experimental tools for the exploration of macromolecular structure and dynamics. Though it has long been recognized that hydrostatic pressure offers a complementary and often unique view of macromolecular structure, stability and dynamics, it has not been employed nearly as much. For solution NMR applications the limited use of high-pressure is undoubtedly traced to difficulties of employing pressure in the context of modern multinuclear and multidimensional NMR. Limitations in pressure tolerant NMR sample cells have been overcome and enable detailed studies of macromolecular energy landscapes, hydration, dynamics and function. Here we review the practical considerations for studies of biological macromolecules at elevated pressure, with a particular emphasis on applications in protein biophysics and structural biology.
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Affiliation(s)
- José A Caro
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States
| | - A Joshua Wand
- Johnson Research Foundation and Department of Biochemistry and Biophysics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104-6509, United States.
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12
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Jenkins KA, Fossat MJ, Zhang S, Rai DK, Klein S, Gillilan R, White Z, Gerlich G, McCallum SA, Winter R, Gruner SM, Barrick D, Royer CA. The consequences of cavity creation on the folding landscape of a repeat protein depend upon context. Proc Natl Acad Sci U S A 2018; 115:E8153-E8161. [PMID: 30104366 PMCID: PMC6126725 DOI: 10.1073/pnas.1807379115] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The effect of introducing internal cavities on protein native structure and global stability has been well documented, but the consequences of these packing defects on folding free-energy landscapes have received less attention. We investigated the effects of cavity creation on the folding landscape of the leucine-rich repeat protein pp32 by high-pressure (HP) and urea-dependent NMR and high-pressure small-angle X-ray scattering (HPSAXS). Despite a modest global energetic perturbation, cavity creation in the N-terminal capping motif (N-cap) resulted in very strong deviation from two-state unfolding behavior. In contrast, introduction of a cavity in the most stable, C-terminal half of pp32 led to highly concerted unfolding, presumably because the decrease in stability by the mutations attenuated the N- to C-terminal stability gradient present in WT pp32. Interestingly, enlarging the central cavity of the protein led to the population under pressure of a distinct intermediate in which the N-cap and repeats 1-4 were nearly completely unfolded, while the fifth repeat and the C-terminal capping motif remained fully folded. Thus, despite modest effects on global stability, introducing internal cavities can have starkly distinct repercussions on the conformational landscape of a protein, depending on their structural and energetic context.
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Affiliation(s)
- Kelly A Jenkins
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Martin J Fossat
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Durgesh K Rai
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
| | - Sean Klein
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Richard Gillilan
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
| | - Zackary White
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Grayson Gerlich
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Scott A McCallum
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Roland Winter
- Department of Physical Chemistry, Technical University of Dortmund, 44227 Dortmund, Germany
| | - Sol M Gruner
- Cornell High Energy Synchrotron Source, Cornell University, Ithaca, NY 14853
- Department of Physics, Cornell University, Ithaca, NY 14853
- Kavli Institute at Cornell for Nanoscale Science, Cornell University, Ithaca, NY 14853
| | - Doug Barrick
- T. C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218
| | - Catherine A Royer
- Graduate Program in Biochemistry and Biophysics, Rensselaer Polytechnic Institute, Troy, NY 12180;
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180
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13
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Roche J, Royer CA, Roumestand C. Monitoring protein folding through high pressure NMR spectroscopy. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2017; 102-103:15-31. [PMID: 29157491 DOI: 10.1016/j.pnmrs.2017.05.003] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 05/31/2017] [Accepted: 05/31/2017] [Indexed: 06/07/2023]
Abstract
High-pressure is a well-known perturbation method used to destabilize globular proteins. It is perfectly reversible, which is essential for a proper thermodynamic characterization of a protein equilibrium. In contrast to other perturbation methods such as heat or chemical denaturant that destabilize protein structures uniformly, pressure exerts local effects on regions or domains of a protein containing internal cavities. When combined with NMR spectroscopy, hydrostatic pressure offers the possibility to monitor at a residue level the structural transitions occurring upon unfolding and to determine the kinetic properties of the process. High-pressure NMR experiments can now be routinely performed, owing to the recent development of commercially available high-pressure sample cells. This review summarizes recent advances and some future directions of high-pressure NMR techniques for the characterization at atomic resolution of the energy landscape of protein folding.
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Affiliation(s)
- Julien Roche
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Christian Roumestand
- Centre de Biochimie Structural INSERM U1054, CNRS UMMR 5058, Université de Montpellier, Montpellier 34090, France.
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14
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Rajasekaran N, Sekhar A, Naganathan AN. A Universal Pattern in the Percolation and Dissipation of Protein Structural Perturbations. J Phys Chem Lett 2017; 8:4779-4784. [PMID: 28910120 DOI: 10.1021/acs.jpclett.7b02021] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Understanding the extent to which information is transmitted through the intramolecular interaction network of proteins upon a perturbation, that is, an allosteric effect, has long remained an unsolved problem. Through an analysis of high-resolution NMR data from the literature on 28 different proteins and 49 structural perturbations, we show that the extent of induced structural changes through mutations and molecular events including protein-protein, protein-peptide, protein-ligand binding, and post-translational modifications exhibit a near-universal exponential functional form. The extent of percolation into the protein structures can be up to 20-25 Å despite no apparent change in the 3D structures. These observations are also consistent with theoretical expectations, elementary graph theoretic analysis of protein structures, detailed molecular dynamics simulations, and experimental double-mutant cycles. Our analysis highlights that most molecular events would contribute to allosteric effects independent of protein structure, topology, or identity and provides a simple avenue to test and potentially model their effects.
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Affiliation(s)
- Nandakumar Rajasekaran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
| | - Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry, and Chemistry, The University of Toronto , Toronto, Ontario M5S 1A8, Canada
| | - Athi N Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras , Chennai 600036, India
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15
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Zwarycz AS, Fossat M, Akanyeti O, Lin Z, Rosenman DJ, Garcia AE, Royer CA, Mills KV, Wang C. V67L Mutation Fills an Internal Cavity To Stabilize RecA Mtu Intein. Biochemistry 2017; 56:2715-2722. [PMID: 28488863 DOI: 10.1021/acs.biochem.6b01264] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inteins mediate protein splicing, which has found extensive applications in protein science and biotechnology. In the Mycobacterium tuberculosis RecA mini-mini intein (ΔΔIhh), a single valine to leucine substitution at position 67 (V67L) dramatically increases intein stability and activity. However, crystal structures show that the V67L mutation causes minimal structural rearrangements, with a root-mean-square deviation of 0.2 Å between ΔΔIhh-V67 and ΔΔIhh-L67. Thus, the structural mechanisms for V67L stabilization and activation remain poorly understood. In this study, we used intrinsic tryptophan fluorescence, high-pressure nuclear magnetic resonance (NMR), and molecular dynamics (MD) simulations to probe the structural basis of V67L stabilization of the intein fold. Guanidine hydrochloride denaturation monitored by fluorescence yielded free energy changes (ΔGf°) of -4.4 and -6.9 kcal mol-1 for ΔΔIhh-V67 and ΔΔIhh-L67, respectively. High-pressure NMR showed that ΔΔIhh-L67 is more resistant to pressure-induced unfolding than ΔΔIhh-V67 is. The change in the volume of folding (ΔVf) was significantly larger for V67 (71 ± 2 mL mol-1) than for L67 (58 ± 3 mL mol-1) inteins. The measured difference in ΔVf (13 ± 3 mL mol-1) roughly corresponds to the volume of the additional methylene group for Leu, supporting the notion that the V67L mutation fills a nearby cavity to enhance intein stability. In addition, we performed MD simulations to show that V67L decreases side chain dynamics and conformational entropy at the active site. It is plausible that changes in cavities in V67L can also mediate allosteric effects to change active site dynamics and enhance intein activity.
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Affiliation(s)
- Allison S Zwarycz
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Martin Fossat
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Otar Akanyeti
- Department of Computer Science, Aberystwyth University , Ceredigion SY23 3FL, Wales, U.K
| | - Zhongqian Lin
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - David J Rosenman
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Angel E Garcia
- Center of Nonlinear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Kenneth V Mills
- Department of Chemistry, College of the Holy Cross , Worcester, Massachusetts 01610, United States
| | - Chunyu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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16
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Rajasekaran N, Suresh S, Gopi S, Raman K, Naganathan AN. A General Mechanism for the Propagation of Mutational Effects in Proteins. Biochemistry 2016; 56:294-305. [DOI: 10.1021/acs.biochem.6b00798] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nandakumar Rajasekaran
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | | | - Soundhararajan Gopi
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Karthik Raman
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Athi N. Naganathan
- Department of Biotechnology, Bhupat & Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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17
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Bellissent-Funel MC, Hassanali A, Havenith M, Henchman R, Pohl P, Sterpone F, van der Spoel D, Xu Y, Garcia AE. Water Determines the Structure and Dynamics of Proteins. Chem Rev 2016; 116:7673-97. [PMID: 27186992 DOI: 10.1021/acs.chemrev.5b00664] [Citation(s) in RCA: 528] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Water is an essential participant in the stability, structure, dynamics, and function of proteins and other biomolecules. Thermodynamically, changes in the aqueous environment affect the stability of biomolecules. Structurally, water participates chemically in the catalytic function of proteins and nucleic acids and physically in the collapse of the protein chain during folding through hydrophobic collapse and mediates binding through the hydrogen bond in complex formation. Water is a partner that slaves the dynamics of proteins, and water interaction with proteins affect their dynamics. Here we provide a review of the experimental and computational advances over the past decade in understanding the role of water in the dynamics, structure, and function of proteins. We focus on the combination of X-ray and neutron crystallography, NMR, terahertz spectroscopy, mass spectroscopy, thermodynamics, and computer simulations to reveal how water assist proteins in their function. The recent advances in computer simulations and the enhanced sensitivity of experimental tools promise major advances in the understanding of protein dynamics, and water surely will be a protagonist.
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Affiliation(s)
| | - Ali Hassanali
- International Center for Theoretical Physics, Condensed Matter and Statistical Physics 34151 Trieste, Italy
| | - Martina Havenith
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Richard Henchman
- Manchester Institute of Biotechnology The University of Manchester , 131 Princess Street, Manchester M1 7DN, United Kingdom
| | - Peter Pohl
- Johannes Kepler University , Gruberstrasse, 40 4020 Linz, Austria
| | - Fabio Sterpone
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Théorique 13 Rue Pierre et Marie Curie, 75005 Paris, France
| | - David van der Spoel
- Department of Cell and Molecular Biology, Computational and Systems Biology, Uppsala University , 751 24 Uppsala, Sweden
| | - Yao Xu
- Ruhr-Universität Bochum , Faculty of Chemistry and Biochemistry Universitätsstraße 150 Building NC 7/72, D-44780 Bochum, Germany
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory , Los Alamos, New Mexico 87545, United States
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18
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McClelland LJ, Bowler BE. Lower Protein Stability Does Not Necessarily Increase Local Dynamics. Biochemistry 2016; 55:2681-93. [DOI: 10.1021/acs.biochem.5b01060] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Levi J. McClelland
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
| | - Bruce E. Bowler
- Department of Chemistry & Biochemistry, Center for Biomolecular Structure and Dynamics, University of Montana, Missoula, Montana 59812, United States
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19
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Dellarole M, Caro JA, Roche J, Fossat M, Barthe P, García-Moreno E B, Royer CA, Roumestand C. Evolutionarily Conserved Pattern of Interactions in a Protein Revealed by Local Thermal Expansion Properties. J Am Chem Soc 2015; 137:9354-62. [PMID: 26135981 DOI: 10.1021/jacs.5b04320] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The way in which the network of intramolecular interactions determines the cooperative folding and conformational dynamics of a protein remains poorly understood. High-pressure NMR spectroscopy is uniquely suited to examine this problem because it combines the site-specific resolution of the NMR experiments with the local character of pressure perturbations. Here we report on the temperature dependence of the site-specific volumetric properties of various forms of staphylococcal nuclease (SNase), including three variants with engineered internal cavities, as measured with high-pressure NMR spectroscopy. The strong temperature dependence of pressure-induced unfolding arises from poorly understood differences in thermal expansion between the folded and unfolded states. A significant inverse correlation was observed between the global thermal expansion of the folded proteins and the number of strong intramolecular hydrogen bonds, as determined by the temperature coefficient of the backbone amide chemical shifts. Comparison of the identity of these strong H-bonds with the co-evolution of pairs of residues in the SNase protein family suggests that the architecture of the interactions detected in the NMR experiments could be linked to a functional aspect of the protein. Moreover, the temperature dependence of the residue-specific volume changes of unfolding yielded residue-specific differences in expansivity and revealed how mutations impact intramolecular interaction patterns. These results show that intramolecular interactions in the folded states of proteins impose constraints against thermal expansion and that, hence, knowledge of site-specific thermal expansivity offers insight into the patterns of strong intramolecular interactions and other local determinants of protein stability, cooperativity, and potentially also of function.
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Affiliation(s)
- Mariano Dellarole
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Jose A Caro
- ‡T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.. Baltimore, Maryland 21218, United States
| | - Julien Roche
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Martin Fossat
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Philippe Barthe
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Bertrand García-Moreno E
- ‡T. C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 N. Charles St.. Baltimore, Maryland 21218, United States
| | - Catherine A Royer
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
| | - Christian Roumestand
- †Centre de Biochimie Structurale, CNRS UMR5048, INSERM U554, Université Montpellier 1, 29 rue de Navacelles, Montpellier, France 34090
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20
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Roche J, Dellarole M, Royer CA, Roumestand C. Exploring the Protein Folding Pathway with High-Pressure NMR: Steady-State and Kinetics Studies. Subcell Biochem 2015; 72:261-278. [PMID: 26174386 DOI: 10.1007/978-94-017-9918-8_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Defining the physical-chemical determinants of protein folding and stability, under normal and pathological conditions has constituted a major subfield in biophysical chemistry for over 50 years. Although a great deal of progress has been made in recent years towards this goal, a number of important questions remain. These include characterizing the structural, thermodynamic and dynamic properties of the barriers between conformational states on the protein energy landscape, understanding the sequence dependence of folding cooperativity, defining more clearly the role of solvation in controlling protein stability and dynamics and probing the high energy thermodynamic states in the native state basin and their role in misfolding and aggregation. Fundamental to the elucidation of these questions is a complete thermodynamic parameterization of protein folding determinants. In this chapter, we describe the use of high-pressure coupled to Nuclear Magnetic Resonance (NMR) spectroscopy to reveal unprecedented details on the folding energy landscape of proteins.
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Affiliation(s)
- Julien Roche
- Centre de Biochimie Structurale, UMR UM1&UM2/5048 CNRS/1054 INSERM, 29 rue de Navacelles, 34090, Montpellier, France
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21
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Affiliation(s)
- Jeffrey L Brodsky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA; and
| | - Patricia L Clark
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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22
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Silva JL, Oliveira AC, Vieira TCRG, de Oliveira GAP, Suarez MC, Foguel D. High-Pressure Chemical Biology and Biotechnology. Chem Rev 2014; 114:7239-67. [DOI: 10.1021/cr400204z] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Andrea C. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Guilherme A. P. de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Marisa C. Suarez
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
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23
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Elahi M, Islam MM, Noguchi K, Yohda M, Toh H, Kuroda Y. Computational prediction and experimental characterization of a "size switch type repacking" during the evolution of dengue envelope protein domain III (ED3). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:585-92. [PMID: 24373879 DOI: 10.1016/j.bbapap.2013.12.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/17/2013] [Accepted: 12/19/2013] [Indexed: 11/16/2022]
Abstract
Dengue viruses (DEN) are classified into four serotypes (DEN1-DEN4) exhibiting high sequence and structural similarities, and infections by multiple serotypes can lead to the deadly dengue hemorrhagic fever. Here, we aim at characterizing the thermodynamic stability of DEN envelope protein domain III (ED3) during its evolution, and we report a structural analysis of DEN4wt ED3 combined with a systematic mutational analysis of residues 310 and 387. Molecular modeling based on our DEN3 and DEN4 ED3 structures indicated that the side-chains of residues 310/387, which are Val(310)/Ile(387) and Met(310)/Leu(387) in DEN3wt and DEN4wt, respectively, could be structurally compensated, and that a "size switch type repacking" might have occurred at these sites during the evolution of DEN into its four serotypes. This was experimentally confirmed by a 10°C and 5°C decrease in the thermal stability of, respectively, DEN3 ED3 variants with Met(310)/Ile(387) and Val(310)/Leu(387), whereas the variant with Met(310)/Leu(387), which contains a double mutation, had the same stability as the wild type DEN3. Namely, the Met310Val mutation should have preceded the Leu387Ile mutation in order to maintain the tight internal packing of ED3 and thus its thermodynamic stability. This view was confirmed by a phylogenetic reconstruction indicating that a common DEN ancestor would have Met(310)/Leu(387), and the intermediate node protein, Val(310)/Leu(387), which then mutated to the Val(310)/Ile(387) pair found in the present DEN3. The hypothesis was further confirmed by the observation that all of the present DEN viruses exhibit only stabilizing amino acid pairs at the 310/387 sites.
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Affiliation(s)
- Montasir Elahi
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Monirul M Islam
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Keiichi Noguchi
- Instrumentation Analysis Center, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Masafumi Yohda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan
| | - Hiroyuki Toh
- Computational Biology Research Center, AIST Tokyo Waterfront Bio-IT Research Building, 2-4-7 Aomi, Koto-ku, Tokyo, 135-0064, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture & Technology, Nakamachi, Koganei-shi, Tokyo 184-8588, Japan.
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24
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Conformational selection and adaptation to ligand binding in T4 lysozyme cavity mutants. Proc Natl Acad Sci U S A 2013; 110:E4306-15. [PMID: 24167295 DOI: 10.1073/pnas.1318754110] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The studies presented here explore the relationship between protein packing and molecular flexibility using ligand-binding cavity mutants of T4 lysozyme. Although previously reported crystal structures of the mutants investigated show single conformations that are similar to the WT protein, site-directed spin labeling in solution reveals additional conformational substates in equilibrium exchange with a WT-like population. Remarkably, binding of ligands, including the general anesthetic halothane shifts the population to the WT-like state, consistent with a conformational selection model of ligand binding, but structural adaptation to the ligand is also apparent in one mutant. Distance mapping with double electron-electron resonance spectroscopy and the absence of ligand binding suggest that the new substates induced by the cavity-creating mutations represent alternate packing modes in which the protein fills or partially fills the cavity with side chains, including the spin label in one case; external ligands compete with the side chains for the cavity space, stabilizing the WT conformation. The results have implications for mechanisms of anesthesia, the response of proteins to hydrostatic pressure, and protein engineering.
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25
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Roche J, Dellarole M, Caro JA, Norberto DR, Garcia AE, Garcia-Moreno B, Roumestand C, Royer CA. Effect of Internal Cavities on Folding Rates and Routes Revealed by Real-Time Pressure-Jump NMR Spectroscopy. J Am Chem Soc 2013; 135:14610-8. [DOI: 10.1021/ja406682e] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Julien Roche
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - Mariano Dellarole
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - José A. Caro
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Douglas R. Norberto
- Department
of Biochemistry, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Angel E. Garcia
- Department
of Physics and Applied Physics and Center for Biotechnology and Interdisciplinary
Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Bertrand Garcia-Moreno
- Department
of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Christian Roumestand
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
| | - Catherine A. Royer
- Centre de Biochimie
Structurale, INSERM U554, CNRS UMR 5048, Universités de Montpellier, France
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