1
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Sun Q, Fu Y, Wang W. Temperature effects on hydrophobic interactions: Implications for protein unfolding. Chem Phys 2022. [DOI: 10.1016/j.chemphys.2022.111550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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2
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Kunka A, Lacko D, Stourac J, Damborsky J, Prokop Z, Mazurenko S. CalFitter 2.0: Leveraging the power of singular value decomposition to analyse protein thermostability. Nucleic Acids Res 2022; 50:W145-W151. [PMID: 35580052 PMCID: PMC9252748 DOI: 10.1093/nar/gkac378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/20/2022] [Accepted: 05/14/2022] [Indexed: 11/24/2022] Open
Abstract
The importance of the quantitative description of protein unfolding and aggregation for the rational design of stability or understanding the molecular basis of protein misfolding diseases is well established. Protein thermostability is typically assessed by calorimetric or spectroscopic techniques that monitor different complementary signals during unfolding. The CalFitter webserver has already proved integral to deriving invaluable energy parameters by global data analysis. Here, we introduce CalFitter 2.0, which newly incorporates singular value decomposition (SVD) of multi-wavelength spectral datasets into the global fitting pipeline. Processed time- or temperature-evolved SVD components can now be fitted together with other experimental data types. Moreover, deconvoluted basis spectra provide spectral fingerprints of relevant macrostates populated during unfolding, which greatly enriches the information gains of the CalFitter output. The SVD analysis is fully automated in a highly interactive module, providing access to the results to users without any prior knowledge of the underlying mathematics. Additionally, a novel data uploading wizard has been implemented to facilitate rapid and easy uploading of multiple datasets. Together, the newly introduced changes significantly improve the user experience, making this software a unique, robust, and interactive platform for the analysis of protein thermal denaturation data. The webserver is freely accessible at https://loschmidt.chemi.muni.cz/calfitter.
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Affiliation(s)
- Antonin Kunka
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - David Lacko
- Faculty of Information Technology, Brno University of Technology, Brno, Czech Republic
| | - Jan Stourac
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Jiri Damborsky
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Zbynek Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Stanislav Mazurenko
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Brno, Czech Republic.,International Centre for Clinical Research, St. Anne's University Hospital Brno, Brno, Czech Republic
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3
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Bitonti A, Puglisi R, Meli M, Martin SR, Colombo G, Temussi PA, Pastore A. Recipes for Inducing Cold Denaturation in an Otherwise Stable Protein. J Am Chem Soc 2022; 144:7198-7207. [PMID: 35427450 PMCID: PMC9052743 DOI: 10.1021/jacs.1c13355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Although cold denaturation
is a fundamental phenomenon common to
all proteins, it can only be observed in a handful of cases where
it occurs at temperatures above the freezing point of water. Understanding
the mechanisms that determine cold denaturation and the rules that
permit its observation is an important challenge. A way to approach
them is to be able to induce cold denaturation in an otherwise stable
protein by means of mutations. Here, we studied CyaY, a relatively
stable bacterial protein with no detectable cold denaturation and
a high melting temperature of 54 °C. We have characterized for
years the yeast orthologue of CyaY, Yfh1, a protein that undergoes
cold and heat denaturation at 5 and 35 °C, respectively. We demonstrate
that, by transferring to CyaY the lessons learnt from Yfh1, we can
induce cold denaturation by introducing a restricted number of carefully
designed mutations aimed at destabilizing the overall fold and inducing
electrostatic frustration. We used molecular dynamics simulations
to rationalize our findings and demonstrate the individual effects
observed experimentally with the various mutants. Our results constitute
the first example of rationally designed cold denaturation and demonstrate
the importance of electrostatic frustration on the mechanism of cold
denaturation.
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Affiliation(s)
- Angela Bitonti
- Department of Molecular Medicine, University of Pavia, Via C Forlanini 6, 27100 Pavia, Italy
| | - Rita Puglisi
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
| | - Massimiliano Meli
- Istituto di Scienze e Tecnologie Chimiche “Giulio Natta” (SCITEC), CNR, Via Mario Bianco 9, 20131 Milano, Italy
| | - Stephen R. Martin
- Structural Biology Technology Platform, The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, United Kingdom
| | - Giorgio Colombo
- Department of Chemistry, University of Pavia, Via Torquato Taramelli, 12, Pavia 27100, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King’s College London, London SE5 9RT, United Kingdom
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4
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Pulavarti SVSRK, Maguire JB, Yuen S, Harrison JS, Griffin J, Premkumar L, Esposito EA, Makhatadze GI, Garcia AE, Weiss TM, Snell EH, Kuhlman B, Szyperski T. From Protein Design to the Energy Landscape of a Cold Unfolding Protein. J Phys Chem B 2022; 126:1212-1231. [PMID: 35128921 PMCID: PMC9281400 DOI: 10.1021/acs.jpcb.1c10750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding is crucial for protein sciences. The conformational spaces and energy landscapes of cold (unfolded) protein states, as well as the associated transitions, are hardly explored. Furthermore, it is not known how structure relates to the cooperativity of cold transitions, if cold and heat unfolded states are thermodynamically similar, and if cold states play important roles for protein function. We created the cold unfolding 4-helix bundle DCUB1 with a de novo designed bipartite hydrophilic/hydrophobic core featuring a hydrogen bond network which extends across the bundle in order to study the relative importance of hydrophobic versus hydrophilic protein-water interactions for cold unfolding. Structural and thermodynamic characterization resulted in the discovery of a complex energy landscape for cold transitions, while the heat unfolded state is a random coil. Below ∼0 °C, the core of DCUB1 disintegrates in a largely cooperative manner, while a near-native helical content is retained. The resulting cold core-unfolded state is compact and features extensive internal dynamics. Below -5 °C, two additional cold transitions are seen, that is, (i) the formation of a water-mediated, compact, and highly dynamic dimer, and (ii) the onset of cold helix unfolding decoupled from cold core unfolding. Our results suggest that cold unfolding is initiated by the intrusion of water into the hydrophilic core network and that cooperativity can be tuned by varying the number of core hydrogen bond networks. Protein design has proven to be invaluable to explore the energy landscapes of cold states and to robustly test related theories.
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Affiliation(s)
- Surya V S R K Pulavarti
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Jack B Maguire
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Shirley Yuen
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Joseph S Harrison
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Jermel Griffin
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Lakshmanane Premkumar
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Edward A Esposito
- Malvern Panalytical Inc, Northhampton, Massachsetts 01060, United States
| | - George I Makhatadze
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 08544, United States
| | - Angel E Garcia
- Center for Non Linear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Thomas M Weiss
- Stanford Synchrotron Radiation Lightsource, Stanford Linear Accelerator Center, Stanford University, Menlo Park, California 94025, United States
| | - Edward H Snell
- Hauptman-Woodward Medical Research Institute, 700 Ellicott Street, Buffalo, New York 14203, United States.,Department of Materials Design and Innovation, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
| | - Brian Kuhlman
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Thomas Szyperski
- Department of Chemistry, University at Buffalo, The State University of New York, Buffalo, New York 14260, United States
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5
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Tejaswi Naidu K, Prakash Prabhu N. An able-cryoprotectant and a moderate denaturant: distinctive character of ethylene glycol on protein stability. J Biomol Struct Dyn 2022; 40:820-832. [DOI: 10.1080/07391102.2020.1819422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- K. Tejaswi Naidu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - N. Prakash Prabhu
- Department of Biotechnology & Bioinformatics, School of Life Sciences, University of Hyderabad, Hyderabad, India
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6
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Gomes DC, Teixeira SCM, Leão JB, Razinkov VI, Qi W, Rodrigues MA, Roberts CJ. In Situ Monitoring of Protein Unfolding/Structural States under Cold High-Pressure Stress. Mol Pharm 2021; 18:4415-4427. [PMID: 34699230 DOI: 10.1021/acs.molpharmaceut.1c00604] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Biopharmaceutical formulations may be compromised by freezing, which has been attributed to protein conformational changes at a low temperature, and adsorption to ice-liquid interfaces. However, direct measurements of unfolding/conformational changes in sub-0 °C environments are limited because at ambient pressure, freezing of water can occur, which limits the applicability of otherwise commonly used analytical techniques without specifically tailored instrumentation. In this report, small-angle neutron scattering (SANS) and intrinsic fluorescence (FL) were used to provide in situ analysis of protein tertiary structure/folding at temperatures as low as -15 °C utilizing a high-pressure (HP) environment (up to 3 kbar) that prevents water from freezing. The results show that the α-chymotrypsinogen A (aCgn) structure is reasonably maintained under acidic pH (and corresponding pD) for all conditions of pressure and temperature tested. On the other hand, reversible structural changes and formation of oligomeric species were detected near -10 °C via HP-SANS for ovalbumin under neutral pD conditions. This was found to be related to the proximity of the temperature of cold denaturation of ovalbumin (TCD ∼ -17 °C; calculated via isothermal chemical denaturation and Gibbs-Helmholtz extrapolation) rather than a pressure effect. Significant structural changes were also observed for a monoclonal antibody, anti-streptavidin IgG1 (AS-IgG1), under acidic conditions near -5 °C and a pressure of ∼2 kbar. The conformational perturbation detected for AS-IgG1 is proposed to be consistent with the formation of unfolding intermediates such as molten globule states. Overall, the in situ approaches described here offer a means to characterize the conformational stability of biopharmaceuticals and proteins more generally under cold-temperature stress by the assessment of structural alteration, self-association, and reversibility of each process. This offers an alternative to current ex situ methods that are based on higher temperatures and subsequent extrapolation of the data and interpretations to the cold-temperature regime.
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Affiliation(s)
- Diana C Gomes
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal.,Department of Chemical and Biomolecular Engineering, University of Delaware, 590 Avenue 1743, Newark, Delaware 19713, United States
| | - Susana C M Teixeira
- Department of Chemical and Biomolecular Engineering, University of Delaware, 590 Avenue 1743, Newark, Delaware 19713, United States.,NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Juscelino B Leão
- NIST Center for Neutron Research, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
| | - Vladimir I Razinkov
- Drug Product Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Wei Qi
- Drug Product Development, Amgen Inc., Thousand Oaks, California 91320, United States
| | - Miguel A Rodrigues
- Centro de Química Estrutural, Departamento de Engenharia Química, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001 Lisboa, Portugal
| | - Christopher J Roberts
- Department of Chemical and Biomolecular Engineering, University of Delaware, 590 Avenue 1743, Newark, Delaware 19713, United States
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7
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Bansal R, Jha SK, Jha NK. Size-based Degradation of Therapeutic Proteins - Mechanisms, Modelling and Control. Biomol Concepts 2021; 12:68-84. [PMID: 34146465 DOI: 10.1515/bmc-2021-0008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/07/2021] [Indexed: 02/02/2023] Open
Abstract
Protein therapeutics are in great demand due to their effectiveness towards hard-to-treat diseases. Despite their high demand, these bio-therapeutics are very susceptible to degradation via aggregation, fragmentation, oxidation, and reduction, all of which are very likely to affect the quality and efficacy of the product. Mechanisms and modelling of these degradation (aggregation and fragmentation) pathways is critical for gaining a deeper understanding of stability of these products. This review aims to provide a summary of major developments that have occurred towards unravelling the mechanisms of size-based protein degradation (particularly aggregation and fragmentation), modelling of these size-based degradation pathways, and their control. Major caveats that remain in our understanding and control of size-based protein degradation have also been presented and discussed.
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Affiliation(s)
- Rohit Bansal
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, Uttar Pradesh, India
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8
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Harish B, Gillilan RE, Zou J, Wang J, Raleigh DP, Royer CA. Protein unfolded states populated at high and ambient pressure are similarly compact. Biophys J 2021; 120:2592-2598. [PMID: 33961866 DOI: 10.1016/j.bpj.2021.04.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 04/23/2021] [Accepted: 04/29/2021] [Indexed: 10/21/2022] Open
Abstract
The relationship between the dimensions of pressure-unfolded states of proteins compared with those at ambient pressure is controversial; resolving this issue is related directly to the mechanisms of pressure denaturation. Moreover, a significant pressure dependence of the compactness of unfolded states would complicate the interpretation of folding parameters from pressure perturbation and make comparison to those obtained using alternative perturbation approaches difficult. Here, we determined the compactness of the pressure-unfolded state of a small, cooperatively folding model protein, CTL9-I98A, as a function of temperature. This protein undergoes both thermal unfolding and cold denaturation, and the temperature dependence of the compactness at atmospheric pressure is known. High-pressure small angle x-ray scattering studies, yielding the radius of gyration and high-pressure diffusion ordered spectroscopy NMR experiments, yielding the hydrodynamic radius were carried out as a function of temperature at 250 MPa, a pressure at which the protein is unfolded. The radius of gyration values obtained at any given temperature at 250 MPa were similar to those reported previously at ambient pressure, and the trends with temperature are similar as well, although the pressure-unfolded state appears to undergo more pronounced expansion at high temperature than the unfolded state at atmospheric pressure. At 250 MPa, the compaction of the unfolded chain was maximal between 25 and 30°C, and the chain expanded upon both cooling and heating. These results reveal that the pressure-unfolded state of this protein is very similar to that observed at ambient pressure, demonstrating that pressure perturbation represents a powerful approach for observing the unfolded states of proteins under otherwise near-native conditions.
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Affiliation(s)
| | | | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Jinqiu Wang
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Catherine A Royer
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
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9
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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.
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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
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10
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Stenzoski NE, Zou J, Piserchio A, Ghose R, Holehouse AS, Raleigh DP. The Cold-Unfolded State Is Expanded but Contains Long- and Medium-Range Contacts and Is Poorly Described by Homopolymer Models. Biochemistry 2020; 59:3290-3299. [PMID: 32786415 DOI: 10.1021/acs.biochem.0c00469] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cold unfolding of proteins is predicted by the Gibbs-Helmholtz equation and is thought to be driven by a strongly temperature-dependent interaction of protein nonpolar groups with water. Studies of the cold-unfolded state provide insight into protein energetics, partially structured states, and folding cooperativity and are of practical interest in biotechnology. However, structural characterization of the cold-unfolded state is much less extensive than studies of thermally or chemically denatured unfolded states, in large part because the midpoint of the cold unfolding transition is usually below freezing. We exploit a rationally designed point mutation (I98A) in the hydrophobic core of the C-terminal domain of the ribosomal protein L9 that allows the cold denatured state ensemble to be observed above 0 °C at near neutral pH and ambient pressure in the absence of added denaturants. A combined approach consisting of paramagnetic relaxation enhancement measurements, analysis of small-angle X-ray scattering data, all-atom simulations, and polymer theory provides a detailed description of the cold-unfolded state. Despite a globally expanded ensemble, as determined by small-angle X-ray scattering, sequence-specific medium- and long-range interactions in the cold-unfolded state give rise to deviations from homopolymer-like behavior. Our results reveal that the cold-denatured state is heterogeneous with local and long-range intramolecular interactions that may prime the folded state and also demonstrate that significant long-range interactions are compatible with expanded unfolded ensembles. The work also highlights the limitations of homopolymer-based descriptions of unfolded states of proteins.
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Affiliation(s)
- Natalie E Stenzoski
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Andrea Piserchio
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States
| | - Ranajeet Ghose
- Department of Chemistry and Biochemistry, The City College of New York, New York, New York 10031, United States.,Graduate Programs in Biochemistry, Chemistry and Physics, The Graduate Center of CUNY, New York, New York 10016, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, United States.,Center for Science and Engineering of Living Systems, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Daniel P Raleigh
- Graduate Program in Biochemistry & Structural Biology, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States.,Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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11
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Wang W, Ohtake S. Science and art of protein formulation development. Int J Pharm 2019; 568:118505. [PMID: 31306712 DOI: 10.1016/j.ijpharm.2019.118505] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023]
Abstract
Protein pharmaceuticals have become a significant class of marketed drug products and are expected to grow steadily over the next decade. Development of a commercial protein product is, however, a rather complex process. A critical step in this process is formulation development, enabling the final product configuration. A number of challenges still exist in the formulation development process. This review is intended to discuss these challenges, to illustrate the basic formulation development processes, and to compare the options and strategies in practical formulation development.
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Affiliation(s)
- Wei Wang
- Biological Development, Bayer USA, LLC, 800 Dwight Way, Berkeley, CA 94710, United States.
| | - Satoshi Ohtake
- Pharmaceutical Research and Development, Pfizer Biotherapeutics Pharmaceutical Sciences, Chesterfield, MO 63017, United States
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12
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Zhang S, Zhang Y, Stenzoski NE, Zou J, Peran I, McCallum SA, Raleigh DP, Royer CA. Pressure-Temperature Analysis of the Stability of the CTL9 Domain Reveals Hidden Intermediates. Biophys J 2019; 116:445-453. [PMID: 30685054 DOI: 10.1016/j.bpj.2019.01.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Revised: 12/13/2018] [Accepted: 01/02/2019] [Indexed: 11/30/2022] Open
Abstract
The observation of two-state unfolding for many small single-domain proteins by denaturants has led to speculation that protein sequences may have evolved to limit the population of partially folded states that could be detrimental to fitness. How such strong cooperativity arises from a multitude of individual interactions is not well understood. Here, we investigate the stability and folding cooperativity of the C-terminal domain of the ribosomal protein L9 in the pressure-temperature plane using site-specific NMR. In contrast to apparent cooperative unfolding detected with denaturant-induced and thermal-induced unfolding experiments and stopped-flow refolding studies at ambient pressure, NMR-detected pressure unfolding revealed significant deviation from two-state behavior, with a core region that was selectively destabilized by increasing temperature. Comparison of pressure-dependent NMR signals from both the folded and unfolded states revealed the population of at least one invisible excited state at atmospheric pressure. The core destabilizing cavity-creating I98A mutation apparently increased the cooperativity of the loss of folded-state peak intensity while also increasing the population of this invisible excited state present at atmospheric pressure. These observations highlight how local stability is subtly modulated by sequence to tune protein conformational landscapes and illustrate the ability of pressure- and temperature-dependent studies to reveal otherwise hidden states.
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Affiliation(s)
- Siwen Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
| | - Yi Zhang
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York
| | - Natalie E Stenzoski
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York
| | - Junjie Zou
- Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York
| | - Ivan Peran
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | | | - Daniel P Raleigh
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Stony Brook, New York; Department of Chemistry, Stony Brook University, Stony Brook, New York; Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York; Institue of Structural and Molecular Biology, University College London, London, United Kingdom.
| | - Catherine A Royer
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, New York; Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York.
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13
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Wang W, Roberts CJ. Protein aggregation – Mechanisms, detection, and control. Int J Pharm 2018; 550:251-268. [DOI: 10.1016/j.ijpharm.2018.08.043] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/18/2018] [Accepted: 08/20/2018] [Indexed: 12/19/2022]
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14
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15
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Stenzoski NE, Luan B, Holehouse AS, Raleigh DP. The Unfolded State of the C-Terminal Domain of L9 Expands at Low but Not at Elevated Temperatures. Biophys J 2018; 115:655-663. [PMID: 30098729 DOI: 10.1016/j.bpj.2018.07.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 07/13/2018] [Accepted: 07/17/2018] [Indexed: 11/26/2022] Open
Abstract
The temperature dependence of the overall dimensions of the denatured state ensemble (DSE) of proteins remains unclear. Some studies indicate compaction of the DSE at high temperatures, whereas others argue that dimensions do not decrease. The degree of compaction or expansion in the cold-denatured state has been less studied. To investigate the temperature dependence of unfolded state dimensions, small angle x-ray scattering measurements were performed in native buffer in the absence of denaturant for a designed point mutant of the C-terminal domain of L9, a small cooperatively folded α-β protein, at 14 different temperatures over the range of 5-60°C. The I98A mutation destabilizes the domain such that both the DSE and the folded state are populated at 25°C in the absence of denaturant or extreme pH. Thermal unfolding as well as cold unfolding can thus be observed in the absence of denaturant, allowing a direct comparison of these regimes for the same protein using the same technique. The temperature of maximal stability, Ts, is 30°C. There is no detectable change in Rg of the unfolded state as the temperature is increased above Ts, but a clear expansion is detected as the temperature is decreased below Ts. The Rg of the DSE populated in buffer was found to be 27.8 ± 1.7 Å at 5°C, 21.8 ± 1.9 Å at 30°C, and 21.7 ± 2.0 Å at 60°C. In contrast, no significant temperature dependence was observed for the value of Rg measured in 6 M guanidine hydrochloride. The small angle x-ray scattering data reported here indicate clear differences between the cold- and thermal-unfolded states and show that there is no significant compaction at elevated temperatures.
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Affiliation(s)
- Natalie E Stenzoski
- Graduate Program in Biochemistry & Structural Biology, Stony Brook, New York
| | - Bowu Luan
- Department of Chemistry, Stony Brook University, Stony Brook, New York
| | - Alex S Holehouse
- Center for Biological Systems Engineering, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Daniel P Raleigh
- Graduate Program in Biochemistry & Structural Biology, Stony Brook, New York; Department of Chemistry, Stony Brook University, Stony Brook, New York; Institute of Structural and Molecular Biology, University of College London, London, United Kingdom.
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16
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Kundu A, Verma PK, Cho M. Effect of Osmolytes on the Conformational Behavior of a Macromolecule in a Cytoplasm-like Crowded Environment: A Femtosecond Mid-IR Pump-Probe Spectroscopy Study. J Phys Chem Lett 2018; 9:724-731. [PMID: 29365266 DOI: 10.1021/acs.jpclett.7b03297] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Osmolytes found endogenously in almost all living beings play an important role in regulating cell volume under harsh environment. Here, to address the longstanding questions about the underlying mechanism of osmolyte effects, we use femtosecond mid-IR pump-probe spectroscopy with two different IR probes that are the OD stretching mode of HDO and the azido stretching mode of azido-derivatized poly(ethylene glycol) dimethyl ether (PEGDME). Our experimental results show that protecting osmolytes bind strongly with water molecules and dehydrate polymer surface, which results in promoting intramolecular interactions of the polymer. By contrast, urea behaves like water molecules without significantly disrupting water H-bonding network and favors extended and random-coil segments of the polymer chain by directly participating in solvation of the polymer. Our findings highlight the importance of direct interaction between urea and macromolecule, while protecting osmolytes indirectly affect the macromolecule through enhancing the water-osmolyte interaction in a crowded environment, which is the case that is often encountered in real biological systems.
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Affiliation(s)
- Achintya Kundu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
| | - Pramod Kumar Verma
- Department of Chemistry, Institute of Science, Banaras Hindu University , Varanasi-221005, India
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) , Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University , Seoul 02841, Republic of Korea
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17
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Rösner HI, Caldarini M, Prestel A, Vanoni MA, Broglia RA, Aliverti A, Tiana G, Kragelund BB. Cold Denaturation of the HIV-1 Protease Monomer. Biochemistry 2017; 56:1029-1032. [DOI: 10.1021/acs.biochem.6b01141] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Heike I. Rösner
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
- Biotech
Research and Innovation Centre (BRIC), Faculty of Health and Medical
Sciences, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Martina Caldarini
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Andreas Prestel
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
| | - Maria A. Vanoni
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Ricardo A. Broglia
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
- Niels Bohr Institute, Blegdamsvej
17, 2100 Copenhagen Ø, Denmark
| | - Alessandro Aliverti
- Department
of Biosciences, University of Milano, via Celoria 26, 20133 Milano, Italy
| | - Guido Tiana
- Department
of Physics, University of Milano and INFN, via Celoria 16, 20133 Milano, Italy
| | - Birthe B. Kragelund
- Structural
Biology and NMR Laboratory (SBiNlab), Department of Biology, University of Copenhagen, Ole Maaloees Vej 5, DK-2200 Copenhagen N, Denmark
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18
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Espinosa YR, Grigera JR, Caffarena ER. Essential dynamics of the cold denaturation: pressure and temperature effects in yeast frataxin. Proteins 2017; 85:125-136. [PMID: 27802581 DOI: 10.1002/prot.25205] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 10/19/2016] [Accepted: 10/25/2016] [Indexed: 11/09/2022]
Abstract
The cold denaturation of globular proteins is a process that can be caused by increasing pressure or decreasing the temperature. Currently, the action mechanism of this process has not been clearly understood, raising an interesting debate on the matter. We have studied the process of cold denaturation using molecular dynamics simulations of the frataxin system Yfh1, which has a dynamic experimental characterization of unfolding at low and high temperatures. The frataxin model here studied allows a comparative analysis using experimental data. Furthermore, we monitored the cold denaturation process of frataxin and also investigated the effect under the high-pressure regime. For a better understanding of the dynamics and structural properties of the cold denaturation, we also analyzed the MD trajectories using essentials dynamic. The results indicate that changes in the structure of water by the effect of pressure and low temperatures destabilize the hydrophobic interaction modifying the solvation and the system volume leading to protein denaturation. Proteins 2016; 85:125-136. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Yanis R Espinosa
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - J Raúl Grigera
- CEQUINOR (CONICET-UNLP), 120 e/61 y 62, Universidad Nacional de La Plata, La Plata, 1900, Argentina
- Departmento de Biología, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, 1900, Argentina
| | - Ernesto R Caffarena
- Fundação Oswaldo Cruz., Rio de Janeiro, Programa de Computação Científica (PROCC), CEP, 21040-360, Rio de Janeiro, Brazil
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19
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Zhang Y, Kitazawa S, Peran I, Stenzoski N, McCallum SA, Raleigh DP, Royer CA. High Pressure ZZ-Exchange NMR Reveals Key Features of Protein Folding Transition States. J Am Chem Soc 2016; 138:15260-15266. [PMID: 27781428 DOI: 10.1021/jacs.6b09887] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding protein folding mechanisms and their sequence dependence requires the determination of residue-specific apparent kinetic rate constants for the folding and unfolding reactions. Conventional two-dimensional NMR, such as HSQC experiments, can provide residue-specific information for proteins. However, folding is generally too fast for such experiments. ZZ-exchange NMR spectroscopy allows determination of folding and unfolding rates on much faster time scales, yet even this regime is not fast enough for many protein folding reactions. The application of high hydrostatic pressure slows folding by orders of magnitude due to positive activation volumes for the folding reaction. We combined high pressure perturbation with ZZ-exchange spectroscopy on two autonomously folding protein domains derived from the ribosomal protein, L9. We obtained residue-specific apparent rates at 2500 bar for the N-terminal domain of L9 (NTL9), and rates at atmospheric pressure for a mutant of the C-terminal domain (CTL9) from pressure dependent ZZ-exchange measurements. Our results revealed that NTL9 folding is almost perfectly two-state, while small deviations from two-state behavior were observed for CTL9. Both domains exhibited large positive activation volumes for folding. The volumetric properties of these domains reveal that their transition states contain most of the internal solvent excluded voids that are found in the hydrophobic cores of the respective native states. These results demonstrate that by coupling it with high pressure, ZZ-exchange can be extended to investigate a large number of protein conformational transitions.
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Affiliation(s)
- Yi Zhang
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Soichiro Kitazawa
- Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Ivan Peran
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Natalie Stenzoski
- Graduate Program in Biochemistry and Structural Biology, Stony Brook University , Stony Brook, New York 11794, United States
| | - Scott A McCallum
- NMR Core Facility, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
| | - Daniel P Raleigh
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794, United States
| | - Catherine A Royer
- Department of Chemistry & Chemical Biology, Rensselaer Polytechnic Institute , Troy, New York 12180, United States.,Department of Biological Sciences, Rensselaer Polytechnic Institute , Troy, New York 12180, United States
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20
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Bothe JR, Tonelli M, Ali IK, Dai Z, Frederick RO, Westler WM, Markley JL. The Complex Energy Landscape of the Protein IscU. Biophys J 2016; 109:1019-25. [PMID: 26331259 PMCID: PMC4564936 DOI: 10.1016/j.bpj.2015.07.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 07/20/2015] [Accepted: 07/28/2015] [Indexed: 11/10/2022] Open
Abstract
IscU, the scaffold protein for iron-sulfur (Fe-S) cluster biosynthesis in Escherichia coli, traverses a complex energy landscape during Fe-S cluster synthesis and transfer. Our previous studies showed that IscU populates two interconverting conformational states: one structured (S) and one largely disordered (D). Both states appear to be functionally important because proteins involved in the assembly or transfer of Fe-S clusters have been shown to interact preferentially with either the S or D state of IscU. To characterize the complex structure-energy landscape of IscU, we employed NMR spectroscopy, small-angle x-ray scattering (SAXS), and differential scanning calorimetry. Results obtained for IscU at pH 8.0 show that its S state is maximally populated at 25°C and that heating or cooling converts the protein toward the D state. Results from NMR and DSC indicate that both the heat- and cold-induced S→D transitions are cooperative and two-state. Low-resolution structural information from NMR and SAXS suggests that the structures of the cold-induced and heat-induced D states are similar. Both states exhibit similar 1H-15N HSQC spectra and the same pattern of peptidyl-prolyl peptide bond configurations by NMR, and both appear to be similarly expanded compared with the S state based on analysis of SAXS data. Whereas in other proteins the cold-denatured states have been found to be slightly more compact than the heat-denatured states, these two states occupy similar volumes in IscU.
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Affiliation(s)
- Jameson R Bothe
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Marco Tonelli
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ibrahim K Ali
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ziqi Dai
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - Ronnie O Frederick
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - William M Westler
- National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin
| | - John L Markley
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin; National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin.
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21
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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: 540] [Impact Index Per Article: 67.5] [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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22
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Chatterjee P, Sengupta N. Signatures of protein thermal denaturation and local hydrophobicity in domain specific hydration behavior: a comparative molecular dynamics study. MOLECULAR BIOSYSTEMS 2016; 12:1139-50. [PMID: 26876051 DOI: 10.1039/c6mb00017g] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We investigate, using atomistic molecular dynamics simulations, the association of surface hydration accompanying local unfolding in the mesophilic protein Yfh1 under a series of thermal conditions spanning its cold and heat denaturation temperatures. The results are benchmarked against the thermally stable protein, Ubq, and behavior at the maximum stability temperature. Local unfolding in Yfh1, predominantly in the beta sheet regions, is in qualitative agreement with recent solution NMR studies; the corresponding Ubq unfolding is not observed. Interestingly, all domains, except for the beta sheet domains of Yfh1, show increased effective surface hydrophobicity with increase in temperature, as reflected by the density fluctuations of the hydration layer. Velocity autocorrelation functions (VACF) of oxygen atoms of water within the hydration layers and the corresponding vibrational density of states (VDOS) are used to characterize alteration in dynamical behavior accompanying the temperature dependent local unfolding. Enhanced caging effects accompanying transverse oscillations of the water molecules are found to occur with the increase in temperature preferentially for the beta sheet domains of Yfh1. Helical domains of both proteins exhibit similar trends in VDOS with changes in temperature. This work demonstrates the existence of key signatures of the local onset of protein thermal denaturation in solvent dynamical behavior.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India.
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23
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Pica A, Graziano G. On the Effect of Sodium Chloride and Sodium Sulfate on Cold Denaturation. PLoS One 2015; 10:e0133550. [PMID: 26197394 PMCID: PMC4511003 DOI: 10.1371/journal.pone.0133550] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/29/2015] [Indexed: 11/28/2022] Open
Abstract
Both sodium chloride and sodium sulfate are able to stabilize yeast frataxin, causing an overall increase of its thermodynamic stability curve, with a decrease in the cold denaturation temperature and an increase in the hot denaturation one. The influence of low concentrations of these two salts on yeast frataxin stability can be assessed by the application of a theoretical model based on scaled particle theory. First developed to figure out the mechanism underlying cold denaturation in water, this model is able to predict the stabilization of globular proteins provided by these two salts. The densities of the salt solutions and their temperature dependence play a fundamental role.
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Affiliation(s)
- Andrea Pica
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Complesso Universitario di Monte Sant’Angelo, Via Cintia – 80126 Napoli, Italy
- Istituto di Biostrutture e Bioimmagini, CNR, Napoli, Italy
| | - Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port’Arsa 11–82100 Benevento, Italy
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24
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Chatterjee P, Bagchi S, Sengupta N. The non-uniform early structural response of globular proteins to cold denaturing conditions: a case study with Yfh1. J Chem Phys 2014; 141:205103. [PMID: 25429964 DOI: 10.1063/1.4901897] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The mechanism of cold denaturation in proteins is often incompletely understood due to limitations in accessing the denatured states at extremely low temperatures. Using atomistic molecular dynamics simulations, we have compared early (nanosecond timescale) structural and solvation properties of yeast frataxin (Yfh1) at its temperature of maximum stability, 292 K (Ts), and the experimentally observed temperature of complete unfolding, 268 K (Tc). Within the simulated timescales, discernible "global" level structural loss at Tc is correlated with a distinct increase in surface hydration. However, the hydration and the unfolding events do not occur uniformly over the entire protein surface, but are sensitive to local structural propensity and hydrophobicity. Calculated infrared absorption spectra in the amide-I region of the whole protein show a distinct red shift at Tc in comparison to Ts. Domain specific calculations of IR spectra indicate that the red shift primarily arises from the beta strands. This is commensurate with a marked increase in solvent accessible surface area per residue for the beta-sheets at Tc. Detailed analyses of structure and dynamics of hydration water around the hydrophobic residues of the beta-sheets show a more bulk water like behavior at Tc due to preferential disruption of the hydrophobic effects around these domains. Our results indicate that in this protein, the surface exposed beta-sheet domains are more susceptible to cold denaturing conditions, in qualitative agreement with solution NMR experimental results.
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Affiliation(s)
- Prathit Chatterjee
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Sayan Bagchi
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
| | - Neelanjana Sengupta
- Physical Chemistry Division, CSIR-National Chemical Laboratory, Pune 411008, India
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25
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Abstract
A theoretical rationalization of the occurrence of cold denaturation for globular proteins was devised, assuming that the effective size of water molecules depends upon temperature [G. Graziano, Phys. Chem. Chem. Phys., 2010, 12, 14245-14252]. In the present work, it is shown that the latter assumption is not necessary. By performing the same type of calculations in water, 40% (by weight) methanol, methanol, and carbon tetrachloride, it emerges that cold denaturation occurs only in water due to the special temperature dependence of its density and the small size of its molecules. These two coupled factors determine the magnitude and the temperature dependence of the stabilizing term that measures the gain in configurational/translational entropy of water molecules upon folding of the protein. This term has to be contrasted with the destabilizing contribution measuring the loss in conformational entropy of the polypeptide chain upon folding.
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Affiliation(s)
- Giuseppe Graziano
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11 - 82100 Benevento, Italy.
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26
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Luan B, Lyle N, Pappu RV, Raleigh DP. Denatured state ensembles with the same radii of gyration can form significantly different long-range contacts. Biochemistry 2013; 53:39-47. [PMID: 24280003 DOI: 10.1021/bi4008337] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Defining the structural, dynamic, and energetic properties of the unfolded state of proteins is critical for an in-depth understanding of protein folding, protein thermodynamics, and protein aggregation. Here we analyze long-range contacts and compactness in two apparently fully unfolded ensembles of the same protein: the acid unfolded state of the C-terminal domain of ribosomal protein L9 in the absence of high concentrations of urea as well as the urea unfolded state at low pH. Small angle X-ray scattering reveals that the two states are expanded with values of Rg differing by <7%. Paramagnetic relaxation enhancement (PRE) nuclear magnetic resonance studies, however, reveal that the acid unfolded state samples conformations that facilitate contacts between residues that are distant in sequence while the urea unfolded state ensemble does not. The experimental PRE profiles for the acid unfolded state differ significantly from these predicted using an excluded volume limit ensemble, but these long-range contacts are largely eliminated by the addition of 8 M urea. The work shows that expanded unfolded states can sample very different distributions of long-range contacts yet still have similar radii of gyration. The implications for protein folding and for the characterization of unfolded states are discussed.
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Affiliation(s)
- Bowu Luan
- Department of Chemistry, Stony Brook University , Stony Brook, New York 11794-3400, United States
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27
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Ramírez-Sarmiento CA, Baez M, Wilson CAM, Babul J, Komives EA, Guixé V. Observation of solvent penetration during cold denaturation of E. coli phosphofructokinase-2. Biophys J 2013; 104:2254-63. [PMID: 23708365 DOI: 10.1016/j.bpj.2013.04.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Revised: 04/07/2013] [Accepted: 04/12/2013] [Indexed: 11/16/2022] Open
Abstract
Phosphofructokinase-2 is a dimeric enzyme that undergoes cold denaturation following a highly cooperative N2 2I mechanism with dimer dissociation and formation of an expanded monomeric intermediate. Here, we use intrinsic fluorescence of a tryptophan located at the dimer interface to show that dimer dissociation occurs slowly, over several hours. We then use hydrogen-deuterium exchange mass spectrometry experiments, performed by taking time points over the cold denaturation process, to measure amide exchange throughout the protein during approach to the cold denatured state. As expected, a peptide corresponding to the dimer interface became more solvent exposed over time at 3°C; unexpectedly, amide exchange increased throughout the protein over time at 3°C. The rate of increase in amide exchange over time at 3°C was the same for each region and equaled the rate of dimer dissociation measured by tryptophan fluorescence, suggesting that dimer dissociation and formation of the cold denatured intermediate occur without appreciable buildup of folded monomer. The observation that throughout the protein amide exchange increases as phosphofructokinase-2 cold denatures provides experimental evidence for theoretical predictions that cold denaturation primarily occurs by solvent penetration into the hydrophobic core of proteins in a sequence-independent manner.
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28
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Aznauryan M, Nettels D, Holla A, Hofmann H, Schuler B. Single-molecule spectroscopy of cold denaturation and the temperature-induced collapse of unfolded proteins. J Am Chem Soc 2013; 135:14040-3. [PMID: 24010673 DOI: 10.1021/ja407009w] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Recent Förster resonance energy transfer (FRET) experiments show that heat-unfolded states of proteins become more compact with increasing temperature. At the same time, NMR results indicate that cold-denatured proteins are more expanded than heat-denatured proteins. To clarify the connection between these observations, we investigated the unfolded state of yeast frataxin, whose cold denaturation occurs at temperatures above 273 K, with single-molecule FRET. This method allows the unfolded state dimensions to be probed not only in the cold- and heat-denatured range but also in between, i.e., in the presence of folded protein, and can thus be used to link the two regimes directly. The results show a continuous compaction of unfolded frataxin from 274 to 320 K, with a slight re-expansion at higher temperatures. Cold- and heat-denatured states are thus essentially two sides of the same coin, and their behavior can be understood within the framework of the overall temperature dependence of the unfolded state dimensions.
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Affiliation(s)
- Mikayel Aznauryan
- Department of Biochemistry, University of Zurich , Winterthurerstrasse 190, 8057 Zurich, Switzerland
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