1
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Stiller JB, Kerns SJ, Hoemberger M, Cho YJ, Otten R, Hagan MF, Kern D. Probing the Transition State in Enzyme Catalysis by High-Pressure NMR Dynamics. Nat Catal 2019; 2:726-734. [PMID: 32159076 DOI: 10.1038/s41929-019-0307-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Protein conformational changes are frequently essential for enzyme catalysis, and in several cases, shown to be the limiting factor for overall catalytic speed. However, a structural understanding of corresponding transition states, needed to rationalize the kinetics, remains obscure due to their fleeting nature. Here, we determine the transition-state ensemble of the rate-limiting conformational transition in the enzyme adenylate kinase, by a synergistic approach between experimental high-pressure NMR relaxation during catalysis and molecular dynamics simulations. By comparing homologous kinases evolved under ambient or high pressure in the deep-sea, we detail transition state ensembles that differ in solvation as directly measured by the pressure dependence of catalysis. Capturing transition-state ensembles begins to complete the catalytic energy landscape that is generally characterized by structures of all intermediates and frequencies of transitions among them.
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Affiliation(s)
- John B Stiller
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
| | - S Jordan Kerns
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Marc Hoemberger
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Young-Jin Cho
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States.,Present addresses: S.J.K. 27 Drydock Ave, Boston MA 02110 , M.H. 225 Binney St, Cambridge, MA 02142, Y.J.C. 733 Concord Ave Cambridge, MA 02138
| | - Renee Otten
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
| | - Michael F Hagan
- Department of Physics, Brandeis University, Waltham, Massachusetts 02452, United States
| | - Dorothee Kern
- Department of Biochemistry and Howard Hughes Medical Institute, Brandeis University, Waltham, Massachusetts 02452, United States
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2
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Roche J, Royer CA, Roumestand C. Exploring Protein Conformational Landscapes Using High-Pressure NMR. Methods Enzymol 2019; 614:293-320. [DOI: 10.1016/bs.mie.2018.07.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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3
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Hu J, Chen T, Wang M, Chan HS, Zhang Z. A critical comparison of coarse-grained structure-based approaches and atomic models of protein folding. Phys Chem Chem Phys 2018; 19:13629-13639. [PMID: 28530269 DOI: 10.1039/c7cp01532a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Structure-based coarse-grained Gō-like models have been used extensively in deciphering protein folding mechanisms because of their simplicity and tractability. Meanwhile, explicit-solvent molecular dynamics (MD) simulations with physics-based all-atom force fields have been applied successfully to simulate folding/unfolding transitions for several small, fast-folding proteins. To explore the degree to which coarse-grained Gō-like models and their extensions to incorporate nonnative interactions are capable of producing folding processes similar to those in all-atom MD simulations, here we systematically compare the computed unfolded states, transition states, and transition paths obtained using coarse-grained models and all-atom explicit-solvent MD simulations. The conformations in the unfolded state in common Gō models are more extended, and are thus more in line with experiment, than those from all-atom MD simulations. Nevertheless, the structural features of transition states obtained by the two types of models are largely similar. In contrast, the folding transition paths are significantly more sensitive to modeling details. In particular, when common Gō-like models are augmented with nonnative interactions, the predicted dimensions of the unfolded conformations become similar to those computed using all-atom MD. With this connection, the large deviations of all-atom MD from simple diffusion theory are likely caused in part by the presence of significant nonnative effects in folding processes modelled by current atomic force fields. The ramifications of our findings to the application of coarse-grained modeling to more complex biomolecular systems are discussed.
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Affiliation(s)
- Jie Hu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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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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5
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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: 25] [Impact Index Per Article: 3.1] [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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6
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Zhang Z, Ouyang Y, Chen T. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms. Phys Chem Chem Phys 2016; 18:31304-31311. [DOI: 10.1039/c6cp06181h] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Combining heterogenous native contact energies and many-body interactions could improve the prediction of Brønsted plots using a structure-based model.
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Affiliation(s)
- Zhuqing Zhang
- College of Life Sciences
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Yanhua Ouyang
- College of Life Sciences
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Tao Chen
- College of Chemistry and Materials Science
- Northwest University
- Xi’an
- China
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7
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Fast-folding proteins under stress. Cell Mol Life Sci 2015; 72:4273-85. [PMID: 26231095 DOI: 10.1007/s00018-015-2002-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 07/07/2015] [Accepted: 07/24/2015] [Indexed: 10/23/2022]
Abstract
Proteins are subject to a variety of stresses in biological organisms, including pressure and temperature, which are the easiest stresses to simulate by molecular dynamics. We discuss the effect of pressure and thermal stress on very-fast-folding model proteins, whose in vitro folding can be fully simulated on computers and compared with experiments. We then discuss experiments that can be used to subject proteins to low- and high-temperature unfolding, as well as low- and high-pressure unfolding. Pressure and temperature are prototypical perturbations that illustrate how close many proteins are to instability, a property that cells can exploit to control protein function. We conclude by reviewing some recent in-cell experiments, and progress being made in simulating and measuring protein stability and function inside live cells.
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8
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Wiebe H, Weinberg N. Theoretical volume profiles as a tool for probing transition states: folding kinetics. J Chem Phys 2014; 140:124105. [PMID: 24697422 DOI: 10.1063/1.4868549] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The mechanism by which conformational changes, particularly folding and unfolding, occur in proteins and other biopolymers has been widely discussed in the literature. Molecular dynamics (MD) simulations of protein folding present a formidable challenge since these conformational changes occur on a time scale much longer than what can be afforded at the current level of computational technology. Transition state (TS) theory offers a more economic description of kinetic properties of a reaction system by relating them to the properties of the TS, or for flexible systems, the TS ensemble (TSE). The application of TS theory to protein folding is limited by ambiguity in the definition of the TSE for this process. We propose to identify the TSE for conformational changes in flexible systems by comparison of its experimentally determined volumetric property, known as the volume of activation, to the structure-specific volume profile of the process calculated using MD. We illustrate this approach by its successful application to unfolding of a model chain system.
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Affiliation(s)
- H Wiebe
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
| | - N Weinberg
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada
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9
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Markiewicz BN, Yang L, Culik RM, Gao YQ, Gai F. How quickly can a β-hairpin fold from its transition state? J Phys Chem B 2014; 118:3317-25. [PMID: 24611730 PMCID: PMC3969101 DOI: 10.1021/jp500774q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Understanding the structural nature
of the free energy bottleneck(s)
encountered in protein folding is essential to elucidating the underlying
dynamics and mechanism. For this reason, several techniques, including
Φ-value analysis, have previously been developed to infer the
structural characteristics of such high free-energy or transition
states. Herein we propose that one (or few) appropriately placed backbone
and/or side chain cross-linkers, such as disulfides, could be used
to populate a thermodynamically accessible conformational state that
mimics the folding transition state. Specifically, we test this hypothesis
on a model β-hairpin, Trpzip4, as its folding mechanism has
been extensively studied and is well understood. Our results show
that cross-linking the two β-strands near the turn region increases
the folding rate by an order of magnitude, to about (500 ns)−1, whereas cross-linking the termini results in a hyperstable β-hairpin
that has essentially the same folding rate as the uncross-linked peptide.
Taken together, these findings suggest that cross-linking is not only
a useful strategy to manipulate folding free energy barriers, as shown
in other studies, but also, in some cases, it can be used to stabilize
a folding transition state analogue and allow for direct assessment
of the folding process on the downhill side of the free energy barrier.
The calculated free energy landscape of the cross-linked Trpzip4 also
supports this picture. An empirical analysis further suggests, when
folding of β-hairpins does not involve a significant free energy
barrier, the folding time (τ) follows a power law dependence
on the number of hydrogen bonds to be formed (nH), namely, τ = τ0nHα, with
τ0 = 20 ns and α = 2.3.
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Affiliation(s)
- Beatrice N Markiewicz
- Department of Chemistry and ‡Department of Biochemistry and Biophysics, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
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10
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Ordu EB, Sessions RB, Clarke AR, Karagüler NG. Effect of surface electrostatic interactions on the stability and folding of formate dehydrogenase from Candida methylica. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.molcatb.2013.05.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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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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12
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Jiang X, Zhong A, Chen C, Huang Y, Xiao Y. Network approach to identify the folding transition states of peptides and proteins. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2012; 86:051901. [PMID: 23214808 DOI: 10.1103/physreve.86.051901] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Revised: 07/15/2012] [Indexed: 06/01/2023]
Abstract
Folding transition states and their structures are crucial in understanding protein folding pathways and folding dynamics. As they cannot be detected directly by experiments due to their instability, many computational methods have been proposed to solve this problem. However, each of these methods can give only one part of the transition state ensemble for a peptide or protein. Here we present a folding-network approach to identify the transition states of peptides or proteins and test it on the β-hairpin peptide trpzip2, with the result that we identify all the folding transition states of tripzip2, which may only be determined separately by other methods. This suggests that the network approach can provide more complete information about the folding transition states, at least for peptides.
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Affiliation(s)
- Xuewei Jiang
- School of Fashion, Wuhan Textile University, Wuhan 430073, Hubei, China
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13
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Stable folding core in the folding transition state of an alpha-helical integral membrane protein. Proc Natl Acad Sci U S A 2011; 108:14133-8. [PMID: 21831834 DOI: 10.1073/pnas.1012594108] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Defining the structural features of a transition state is important in understanding a folding reaction. Here, we use Φ-value and double mutant analyses to probe the folding transition state of the membrane protein bacteriorhodopsin. We focus on the final C-terminal helix, helix G, of this seven transmembrane helical protein. Φ-values could be derived for 12 amino acid residues in helix G, most of which have low or intermediate values, suggesting that native structure is disrupted at these amino acid positions in the transition state. Notably, a cluster of residues between E204 and M209 all have Φ-values close to zero. Disruption of helix G is further confirmed by a low Φ-value of 0.2 between residues T170 on helix F and S226 on helix G, suggesting the absence of a native hydrogen bond between helices F and G. Φ-values for paired mutations involved in four interhelical hydrogen bonds revealed that all but one of these bonds is absent in the transition state. The unstructured helix G contrasts with Φ-values along helix B that are generally high, implying native structure in helix B in the transition state. Thus helix B seems to constitute part of a stable folding nucleus while the consolidation of helix G is a relatively late folding event. Polarization of secondary structure correlates with sequence position, with a structured helix B near the N terminus contrasting with an unstructured C-terminal helix G.
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14
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Casares-Atienza S, Weininger U, Cámara-Artigas A, Balbach J, Garcia-Mira MM. Three-state thermal unfolding of onconase. Biophys Chem 2011; 159:267-74. [PMID: 21840114 DOI: 10.1016/j.bpc.2011.07.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2011] [Revised: 07/18/2011] [Accepted: 07/19/2011] [Indexed: 10/18/2022]
Abstract
Onconase is a member of the ribonuclease A superfamily currently in phase IIIb clinical trials as a treatment for malign mesothelioma due to its cytotoxic activity selective against tumor-cells. In this work, we have studied the equilibrium thermal unfolding of onconase using a combination of several structural and biophysical techniques. Our results indicate that at least one significantly populated intermediate, which implies the exposure of hydrophobic surface and significant changes in the environment around Trp3, occurs during the equilibrium unfolding process of this protein. The intermediate begins to populate at about 30° below the global unfolding temperature, reaching a maximum population of nearly 60%, 10° below the global unfolding temperature.
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Affiliation(s)
- Salvador Casares-Atienza
- Departamento de Química Física, Facultad de Ciencias, Universidad de Granada. Avda. Fuentenueva s/n. 18071 Granada, Spain
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15
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Su Z, Lu D, Liu Z. Refolding of inclusion body proteins from E. coli. METHODS OF BIOCHEMICAL ANALYSIS 2011; 54:319-38. [PMID: 21954784 DOI: 10.1002/9780470939932.ch13] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhiguo Su
- State Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100080, China
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16
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Lin M, Zhang J, Lu HM, Chen R, Liang J. Constrained proper sampling of conformations of transition state ensemble of protein folding. J Chem Phys 2011; 134:075103. [PMID: 21341875 PMCID: PMC3071304 DOI: 10.1063/1.3519056] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 11/03/2010] [Indexed: 11/14/2022] Open
Abstract
Characterizing the conformations of protein in the transition state ensemble (TSE) is important for studying protein folding. A promising approach pioneered by Vendruscolo et al. [Nature (London) 409, 641 (2001)] to study TSE is to generate conformations that satisfy all constraints imposed by the experimentally measured φ values that provide information about the native likeness of the transition states. Faísca et al. [J. Chem. Phys. 129, 095108 (2008)] generated conformations of TSE based on the criterion that, starting from a TS conformation, the probabilities of folding and unfolding are about equal through Markov Chain Monte Carlo (MCMC) simulations. In this study, we use the technique of constrained sequential Monte Carlo method [Lin et al., J. Chem. Phys. 129, 094101 (2008); Zhang et al. Proteins 66, 61 (2007)] to generate TSE conformations of acylphosphatase of 98 residues that satisfy the φ-value constraints, as well as the criterion that each conformation has a folding probability of 0.5 by Monte Carlo simulations. We adopt a two stage process and first generate 5000 contact maps satisfying the φ-value constraints. Each contact map is then used to generate 1000 properly weighted conformations. After clustering similar conformations, we obtain a set of properly weighted samples of 4185 candidate clusters. Representative conformation of each of these cluster is then selected and 50 runs of Markov chain Monte Carlo (MCMC) simulation are carried using a regrowth move set. We then select a subset of 1501 conformations that have equal probabilities to fold and to unfold as the set of TSE. These 1501 samples characterize well the distribution of transition state ensemble conformations of acylphosphatase. Compared with previous studies, our approach can access much wider conformational space and can objectively generate conformations that satisfy the φ-value constraints and the criterion of 0.5 folding probability without bias. In contrast to previous studies, our results show that transition state conformations are very diverse and are far from nativelike when measured in cartesian root-mean-square deviation (cRMSD): the average cRMSD between TSE conformations and the native structure is 9.4 Å for this short protein, instead of 6 Å reported in previous studies. In addition, we found that the average fraction of native contacts in the TSE is 0.37, with enrichment in native-like β-sheets and a shortage of long range contacts, suggesting such contacts form at a later stage of folding. We further calculate the first passage time of folding of TSE conformations through calculation of physical time associated with the regrowth moves in MCMC simulation through mapping such moves to a Markovian state model, whose transition time was obtained by Langevin dynamics simulations. Our results indicate that despite the large structural diversity of the TSE, they are characterized by similar folding time. Our approach is general and can be used to study TSE in other macromolecules.
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Affiliation(s)
- Ming Lin
- Wang Yanan Institute for Studies in Economics, Xiamen University, Xiamen, China
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17
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Ramalho TC, da Cunha EF. Thermodynamic Framework of the Interaction between Protein and Solvent Drives Protein Folding. J Biomol Struct Dyn 2011; 28:645-6; discussion 669-674. [DOI: 10.1080/073911011010524975] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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18
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Rouget JB, Schroer MA, Jeworrek C, Pühse M, Saldana JL, Bessin Y, Tolan M, Barrick D, Winter R, Royer CA. Unique features of the folding landscape of a repeat protein revealed by pressure perturbation. Biophys J 2010; 98:2712-21. [PMID: 20513416 DOI: 10.1016/j.bpj.2010.02.044] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Revised: 02/14/2010] [Accepted: 02/26/2010] [Indexed: 11/29/2022] Open
Abstract
The volumetric properties of proteins yield information about the changes in packing and hydration between various states along the folding reaction coordinate and are also intimately linked to the energetics and dynamics of these conformations. These volumetric characteristics can be accessed via pressure perturbation methods. In this work, we report high-pressure unfolding studies of the ankyrin domain of the Notch receptor (Nank1-7) using fluorescence, small-angle x-ray scattering, and Fourier transform infrared spectroscopy. Both equilibrium and pressure-jump kinetic fluorescence experiments were consistent with a simple two-state folding/unfolding transition under pressure, with a rather small volume change for unfolding compared to proteins of similar molecular weight. High-pressure fluorescence, Fourier transform infrared spectroscopy, and small-angle x-ray scattering measurements revealed that increasing urea over a very small range leads to a more expanded pressure unfolded state with a significant decrease in helical content. These observations underscore the conformational diversity of the unfolded-state basin. The temperature dependence of pressure-jump fluorescence relaxation measurements demonstrated that at low temperatures, the folding transition state ensemble (TSE) lies close in volume to the folded state, consistent with significant dehydration at the barrier. In contrast, the thermal expansivity of the TSE was found to be equivalent to that of the unfolded state, indicating that the interactions that constrain the folded-state thermal expansivity have not been established at the folding barrier. This behavior reveals a high degree of plasticity of the TSE of Nank1-7.
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Affiliation(s)
- Jean-Baptiste Rouget
- Centre de Biochimie Structurale, Institut National de la Santé et de la Recherche Médicale, Centre National de la Recherche Scientifique, Université Montpellier, Montpellier, France
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19
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Cobos ES, Iglesias-Bexiga M, Ruiz-Sanz J, Mateo PL, Luque I, Martinez JC. Thermodynamic Characterization of the Folding Equilibrium of the Human Nedd4-WW4 Domain: At the Frontiers of Cooperative Folding. Biochemistry 2009; 48:8712-20. [DOI: 10.1021/bi9007758] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eva S. Cobos
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Manuel Iglesias-Bexiga
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Javier Ruiz-Sanz
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Pedro L. Mateo
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Irene Luque
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
| | - Jose C. Martinez
- Department of Physical Chemistry and Institute of Biotechnology, Faculty of Sciences, University of Granada, 18071 Granada, Spain
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Reaching the protein folding speed limit with large, sub-microsecond pressure jumps. Nat Methods 2009; 6:515-9. [PMID: 19483692 DOI: 10.1038/nmeth.1336] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2009] [Accepted: 04/13/2009] [Indexed: 11/08/2022]
Abstract
Biomolecules are highly pressure-sensitive, but their dynamics upon return to ambient pressure are often too fast to observe with existing approaches. We describe a sample-efficient method capable of large and very fast pressure drops (<1 nanomole, >2,500 atmospheres and <0.7 microseconds). We validated the method by fluorescence-detected refolding of a genetically engineered lambda repressor mutant from its pressure-denatured state. We resolved barrierless structure formation upon return to ambient pressure; we observed a 2.1 +/- 0.7 microsecond refolding time, which is very close to the 'speed limit' for proteins and much faster than the corresponding temperature-jump refolding of the same protein. The ability to experimentally perform a large and very fast pressure drop opens up a new region of the biomolecular energy landscape for atomic-level simulation.
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Barrick D. What have we learned from the studies of two-state folders, and what are the unanswered questions about two-state protein folding? Phys Biol 2009; 6:015001. [PMID: 19208936 DOI: 10.1088/1478-3975/6/1/015001] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Small proteins with globular structures often fold by simple all-or-none mechanisms, both in an equilibrium and a kinetic sense, despite the very large number of partly folded conformations available. This type of 'two-state' folding will be discussed in terms of experimental tests, underlying molecular mechanisms, and limits to two-state behavior. Factors that appear to be important for two-state folding include topology (sequence distance of contacts in the native structure), molecular cooperativity and local energy distribution. Because their local stability distributions and cooperativities can be dissected and analyzed separately from topological features, recent studies of the folding of symmetric proteins will be discussed as a means to better understand the origins of two-state folding.
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Affiliation(s)
- Doug Barrick
- T C Department of Biophysics, The Johns Hopkins University, 3400 N Charles St, Baltimore, MD 21218, USA.
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Mitra L, Rouget JB, Garcia-Moreno B, Royer CA, Winter R. Towards a quantitative understanding of protein hydration and volumetric properties. Chemphyschem 2009; 9:2715-21. [PMID: 18814170 DOI: 10.1002/cphc.200800405] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Herein, we probe by pressure perturbation calorimetry (PPC) the coefficient of thermal expansion, the volumetric and the hydration properties of variants of a hyperstable variant of staphylococcal nuclease (SNase), Delta+PHS. The temperature-dependent volumetric properties of the folded and unfolded states of the wild-type protein are calculated with previously published data. The present PPC results are used to interpret the volume diagram and expansivity at a molecular level. We conclude that the expansivity of the unfolded state is, to a first approximation, temperature independent, while that of the folded state decreases with increasing temperature. Our data suggest that at low temperature the defining contribution to DeltaV comes mainly from excluded volume differences and DeltaV for unfolding is negative. In contrast, at high temperatures, differential solvation due to the increased exposed surface area of the unfolded state and, in particular, its larger thermal volume linked to the increased conformational dynamics of the unfolded state ensemble takes over and DeltaV for unfolding eventually becomes positive.
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Affiliation(s)
- Lally Mitra
- Dortmund University of Technology, Department of Chemistry, Physical Chemistry I-Biophysical Chemistry, Otto-Hahn Str. 6, 44227 Dortmund, Germany
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Walters J, Milam SL, Clark AC. Practical approaches to protein folding and assembly: spectroscopic strategies in thermodynamics and kinetics. Methods Enzymol 2009; 455:1-39. [PMID: 19289201 DOI: 10.1016/s0076-6879(08)04201-8] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We describe here the use of several spectroscopies, such as fluorescence emission, circular dichroism, and differential quenching by acrylamide, in examining the equilibrium and kinetic folding of proteins. The first section regarding equilibrium techniques provides practical information for determining the conformational stability of a protein. In addition, several equilibrium-folding models are discussed, from two-state monomer to four-state homodimer, providing a comprehensive protocol for interpretation of folding curves. The second section focuses on the experimental design and interpretation of kinetic data, such as burst-phase analysis and exponential fits, used in elucidating kinetic folding pathways. In addition, simulation programs are used routinely to support folding models generated by kinetic experiments, and the fundamentals of simulations are covered.
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Affiliation(s)
- Jad Walters
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina, USA
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