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Grazioso R, García-Viñuales S, D'Abrosca G, Baglivo I, Pedone PV, Milardi D, Fattorusso R, Isernia C, Russo L, Malgieri G. The change of conditions does not affect Ros87 downhill folding mechanism. Sci Rep 2020; 10:21067. [PMID: 33273582 PMCID: PMC7713307 DOI: 10.1038/s41598-020-78008-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 11/19/2020] [Indexed: 11/20/2022] Open
Abstract
Downhill folding has been defined as a unique thermodynamic process involving a conformations ensemble that progressively loses structure with the decrease of protein stability. Downhill folders are estimated to be rather rare in nature as they miss an energetically substantial folding barrier that can protect against aggregation and proteolysis. We have previously demonstrated that the prokaryotic zinc finger protein Ros87 shows a bipartite folding/unfolding process in which a metal binding intermediate converts to the native structure through a delicate barrier-less downhill transition. Significant variation in folding scenarios can be detected within protein families with high sequence identity and very similar folds and for the same sequence by varying conditions. For this reason, we here show, by means of DSC, CD and NMR, that also in different pH and ionic strength conditions Ros87 retains its partly downhill folding scenario demonstrating that, at least in metallo-proteins, the downhill mechanism can be found under a much wider range of conditions and coupled to other different transitions. We also show that mutations of Ros87 zinc coordination sphere produces a different folding scenario demonstrating that the organization of the metal ion core is determinant in the folding process of this family of proteins.
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Affiliation(s)
- Rinaldo Grazioso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | | | - Gianluca D'Abrosca
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Ilaria Baglivo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Paolo Vincenzo Pedone
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Danilo Milardi
- Institute of Crystallography-CNR, Via Paolo Gaifami 18, 95126, Catania, Italy
| | - Roberto Fattorusso
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Carla Isernia
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy
| | - Luigi Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
| | - Gaetano Malgieri
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, Via Vivaldi 43, 81100, Caserta, Italy.
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2
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Tokunaga Y, Yamamori Y, Matubayasi N. Probabilistic analysis for identifying the driving force of protein folding. J Chem Phys 2018; 148:125101. [PMID: 29604891 DOI: 10.1063/1.5019410] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Toward identifying the driving force of protein folding, energetics was analyzed in water for Trp-cage (20 residues), protein G (56 residues), and ubiquitin (76 residues) at their native (folded) and heat-denatured (unfolded) states. All-atom molecular dynamics simulation was conducted, and the hydration effect was quantified by the solvation free energy. The free-energy calculation was done by employing the solution theory in the energy representation, and it was seen that the sum of the protein intramolecular (structural) energy and the solvation free energy is more favorable for a folded structure than for an unfolded one generated by heat. Probabilistic arguments were then developed to determine which of the electrostatic, van der Waals, and excluded-volume components of the interactions in the protein-water system governs the relative stabilities between the folded and unfolded structures. It was found that the electrostatic interaction does not correspond to the preference order of the two structures. The van der Waals and excluded-volume components were shown, on the other hand, to provide the right order of preference at probabilities of almost unity, and it is argued that a useful modeling of protein folding is possible on the basis of the excluded-volume effect.
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Affiliation(s)
- Yoshihiko Tokunaga
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Yu Yamamori
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
| | - Nobuyuki Matubayasi
- Division of Chemical Engineering, Graduate School of Engineering Science, Osaka University, Toyonaka, Osaka 560-8531, Japan
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Claus TK, Zhang J, Martin L, Hartlieb M, Mutlu H, Perrier S, Delaittre G, Barner‐Kowollik C. Stepwise Light‐Induced Dual Compaction of Single‐Chain Nanoparticles. Macromol Rapid Commun 2017; 38. [DOI: 10.1002/marc.201700264] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Revised: 05/31/2017] [Indexed: 11/09/2022]
Affiliation(s)
- Tanja K. Claus
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer ChemistryKarlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces (IBG)Karlsruhe Institute of Technology (KIT) Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Junliang Zhang
- Department of ChemistryThe University of Warwick Warwick CV4 7AL UK
| | - Liam Martin
- Department of ChemistryThe University of Warwick Warwick CV4 7AL UK
| | | | - Hatice Mutlu
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer ChemistryKarlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces (IBG)Karlsruhe Institute of Technology (KIT) Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Sébastien Perrier
- Department of ChemistryThe University of Warwick Warwick CV4 7AL UK
- Faculty of Pharmacy and Pharmaceutical SciencesMonash University 381 Royal Parade Parkville Victoria 3052 Australia
| | - Guillaume Delaittre
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer ChemistryKarlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute of Toxicology and Genetics (ITG)Karlsruhe Institute of Technology (KIT) Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
| | - Christopher Barner‐Kowollik
- Macromolecular ArchitecturesInstitute for Chemical Technology and Polymer ChemistryKarlsruhe Institute of Technology (KIT) Engesserstr. 18 76131 Karlsruhe Germany
- Institute for Biological Interfaces (IBG)Karlsruhe Institute of Technology (KIT) Hermann‐von‐Helmholtz‐Platz 1 Eggenstein‐Leopoldshafen 76344 Germany
- School of Chemistry, Physics and Mechanical EngineeringQueensland University of Technology (QUT) 2 George Street Brisbane QLD 4000 Australia
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4
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Hsu PJ, Cheong SA, Lai SK. Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms. J Chem Phys 2014; 140:204905. [DOI: 10.1063/1.4875802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- P J Hsu
- Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan
| | - S A Cheong
- Division of Physics and Applied Physics, School of Physical and Mathematical Sciences, Nanyang Technological University, 21 Nanyang Link, Singapore 637371, Republic of Singapore
| | - S K Lai
- Complex Liquids Laboratory, Department of Physics, National Central University, Chungli 320 Taiwan
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Choi J, Fujitsuka M, Tojo S, Majima T. Folding Dynamics of Cytochrome c Using Pulse Radiolysis. J Am Chem Soc 2012; 134:13430-5. [DOI: 10.1021/ja304904p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Jungkweon Choi
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Mamoru Fujitsuka
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Sachiko Tojo
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
| | - Tetsuro Majima
- The Institute of Scientific and
Industrial (SANKEN), Osaka University,
Mihogaoka 8-1, Ibaraki, Osaka 567-0047,
Japan
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6
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Silva CH, Taft CA. Stoichiometry of Amino acids Drives Protein Folding? J Biomol Struct Dyn 2011; 28:635-6; discussion 669-674. [DOI: 10.1080/073911011010524970] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Arkun Y, Erman B. Prediction of optimal folding routes of proteins that satisfy the principle of lowest entropy loss: dynamic contact maps and optimal control. PLoS One 2010; 5:e13275. [PMID: 20967269 PMCID: PMC2953502 DOI: 10.1371/journal.pone.0013275] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2010] [Accepted: 09/06/2010] [Indexed: 11/21/2022] Open
Abstract
An optimization model is introduced in which proteins try to evade high energy regions of the folding landscape, and prefer low entropy loss routes during folding. We make use of the framework of optimal control whose convenient solution provides practical and useful insight into the sequence of events during folding. We assume that the native state is available. As the protein folds, it makes different set of contacts at different folding steps. The dynamic contact map is constructed from these contacts. The topology of the dynamic contact map changes during the course of folding and this information is utilized in the dynamic optimization model. The solution is obtained using the optimal control theory. We show that the optimal solution can be cast into the form of a Gaussian Network that governs the optimal folding dynamics. Simulation results on three examples (CI2, Sso7d and Villin) show that folding starts by the formation of local clusters. Non-local clusters generally require the formation of several local clusters. Non-local clusters form cooperatively and not sequentially. We also observe that the optimal controller prefers “zipping” or small loop closure steps during folding. The folding routes predicted by the proposed method bear strong resemblance to the results in the literature.
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Affiliation(s)
- Yaman Arkun
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- * E-mail: (YA); (BE)
| | - Burak Erman
- Department of Chemical and Biological Engineering, Koc University, Istanbul, Turkey
- * E-mail: (YA); (BE)
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8
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Liu F, Maynard C, Scott G, Melnykov A, Hall KB, Gruebele M. A natural missing link between activated and downhill protein folding scenarios. Phys Chem Chem Phys 2010; 12:3542-9. [PMID: 20336253 PMCID: PMC7382783 DOI: 10.1039/b925033f] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We propose protein PTB1 : 4W as a good candidate for engineering into a downhill folder. PTB1 : 4W has a probe-dependent thermal unfolding curve and sub-millisecond T-jump relaxation kinetics on more than one time scale. Its refolding rate in denaturant is a non-linear function of denaturant concentration (curved chevron plot). Yet at high denaturant concentration its unfolding is probe-independent, and the folding kinetics can be fitted to a single exponential decay. The domain appears to fold via a mechanism between downhill folding and activated folding over several small barriers, and when denaturant is added, one of these barriers greatly increases and simplifies the observed folding to apparent two-state kinetics. We predict the simplest free energy function consistent with the thermal denaturation and kinetics experiments by using the singular value Smoluchowski dynamics (SVSD) model. PTB1 : 4W is a natural 'missing link' between downhill and activated folding. We suggest mutations that could move the protein into the downhill folding limit.
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Affiliation(s)
- Feng Liu
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Caroline Maynard
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Gregory Scott
- Department of Chemistry, University of Illinois at Urbana-Champaign, IL 61801, USA
| | - Artem Melnykov
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Kathleen B. Hall
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Martin Gruebele
- Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, IL 61801, USA
- Department of Chemistry, University of Illinois at Urbana-Champaign, IL 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, IL 61801, USA
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9
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Xiong K, Asciutto EK, Madura JD, Asher SA. Salt dependence of an alpha-helical peptide folding energy landscapes. Biochemistry 2009; 48:10818-26. [PMID: 19845367 DOI: 10.1021/bi9014709] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We used CD, UV resonance Raman spectroscopy, and molecular dynamics simulation to examine the impact of salts on the conformational equilibria and the Ramachandran Psi angle (un)folding Gibbs free energy landscape coordinate of a mainly polyalanine alpha-helical peptide, AP of sequence AAAAA(AAARA)(3)A. NaClO(4) stabilizes alpha-helical-like conformations more than does NaCl, which stabilizes more than Na(2)SO(4) at identical ionic strengths. This alpha-helix stabilization ordering is the reverse of the Hofmeister series of anions in their ability to disorder water hydrogen bonding. Much of the NaClO(4) alpha-helix stabilization results from ClO(4)(-) association with the AP terminal -NH(3)(+) groups and Arg side chains. ClO(4)(-) stabilizes 3(10)-helix conformations but destabilizes turn conformations. The decreased Cl(-) and SO(4)(2-) AP alpha-helix stabilization probably results from a decreased association with the Arg and terminal -NH(3)(+) groups. Cl(-) is expected to have a smaller binding affinity and thus stabilizes alpha-helical conformations intermediately between NaClO(4) and Na(2)SO(4). Electrostatic screening stabilizes pi-bulge conformations.
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Affiliation(s)
- Kan Xiong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, USA
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10
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Faísca PFN. The nucleation mechanism of protein folding: a survey of computer simulation studies. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:373102. [PMID: 21832332 DOI: 10.1088/0953-8984/21/37/373102] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The nucleation mechanism of protein folding, originally proposed by Baldwin in the early 1970s, was firstly observed by Shakhnovich and co-workers two decades later in the context of Monte Carlo simulations of a simple lattice model. At about the same time the extensive use of φ-value analysis provided the first experimental evidence that the folding of Chymotrypsin-inhibitor 2, a small single-domain protein, which folds with two-state kinetics, is also driven by a nucleation mechanism. Since then, the nucleation mechanism is generally considered the most common form of folding mechanism amongst two-state proteins. However, recent experimental data has put forward the idea that this may not necessarily be so, since the accuracy of the experimentally determined φ values, which are used to identify the critical (i.e. nucleating) residues, is typically poor. Here, we provide a survey of in silico results on the nucleation mechanism, ranging from simple lattice Monte Carlo to more sophisticated off-lattice molecular dynamics simulations, and discuss them in light of experimental data.
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Affiliation(s)
- Patrícia F N Faísca
- Centro de Física Teórica e Computacional, Universidade de Lisboa, Avenida Professor Gama Pinto 2, 1649-003 Lisboa, Portugal
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11
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Kang TS, Kini RM. Structural determinants of protein folding. Cell Mol Life Sci 2009; 66:2341-61. [PMID: 19367367 PMCID: PMC11115868 DOI: 10.1007/s00018-009-0023-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Revised: 03/07/2009] [Accepted: 03/20/2009] [Indexed: 12/11/2022]
Abstract
The last several decades have seen an explosion of knowledge in the field of structural biology. With critical advances in spectroscopic techniques in examining structures of biomacromolecules, in maturation of molecular biology techniques, as well as vast improvements in computation prowess, protein structures are now being elucidated at an unprecedented rate. In spite of all the recent advances, the protein folding puzzle remains as one of the fundamental biochemical challenges. A facet to this empiric problem is the structural determinants of protein folding. What are the driving forces that pivot a polypeptide chain to a specific conformation amongst the vast conformation space? In this review, we shall discuss some of the structural determinants to protein folding that have been identified in the recent decades.
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Affiliation(s)
- Tse Siang Kang
- The Scripps Research Institute, 10550 North Torrey Pines Road GAC 1200, La Jolla, CA 92037 USA
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Block S4, Singapore, 117543 Singapore
| | - R. Manjunatha Kini
- Department of Biological Sciences, National University of Singapore, 14 Science Drive 4, Block S3 #03-17, Singapore, 117543 Singapore
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Lorenz T, Reinstein J. The influence of proline isomerization and off-pathway intermediates on the folding mechanism of eukaryotic UMP/CMP Kinase. J Mol Biol 2008; 381:443-55. [PMID: 18602116 DOI: 10.1016/j.jmb.2008.06.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2008] [Revised: 05/30/2008] [Accepted: 06/02/2008] [Indexed: 10/22/2022]
Abstract
The globular 22-kDa protein UMP/CMP from Dictyostelium discoideum (UmpK) belongs to the family of nucleoside monophosphate (NMP) kinases. These enzymes not only show high sequence and structure similarities but also share the alpha/beta-fold, a very common protein topology. We investigated the protein folding mechanism of UmpK as a representative for this ubiquitous enzyme class. Equilibrium stability towards urea and the unfolding and refolding kinetics were studied by means of fluorescence and far-UV CD spectroscopy. Although the unfolding can be described by a two-state process, folding kinetics are rather complex with four refolding phases that can be resolved and an additional burst phase. Moreover, two of these phases exhibit a pronounced rollover in the refolding limb that cannot be explained by aggregation. Whilst secondary structure formation is not observed in the burst phase reaction, folding to the native structure is strongly influenced by the slowest phase, since 30% of the alpha-helical CD signal is restored therein. This process can be assigned to proline isomerization and is strongly accelerated by the Escherichia coli peptidyl-prolyl isomerase trigger factor. The analysis of our single-mixing and double-mixing experiments suggests the occurrence of an off-pathway intermediate and an unproductive collapsed structure, which appear to be rate limiting for the folding of UmpK.
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Affiliation(s)
- Thorsten Lorenz
- Department of Biomolecular Mechanisms, Max-Planck-Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
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