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Abstract
AbstractThe dynamics of proteins in solution includes a variety of processes, such as backbone and side-chain fluctuations, interdomain motions, as well as global rotational and translational (i.e. center of mass) diffusion. Since protein dynamics is related to protein function and essential transport processes, a detailed mechanistic understanding and monitoring of protein dynamics in solution is highly desirable. The hierarchical character of protein dynamics requires experimental tools addressing a broad range of time- and length scales. We discuss how different techniques contribute to a comprehensive picture of protein dynamics, and focus in particular on results from neutron spectroscopy. We outline the underlying principles and review available instrumentation as well as related analysis frameworks.
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Mendes LFS, Basso LGM, Kumagai PS, Fonseca-Maldonado R, Costa-Filho AJ. Disorder-to-order transitions in the molten globule-like Golgi Reassembly and Stacking Protein. Biochim Biophys Acta Gen Subj 2018; 1862:855-865. [PMID: 29339081 DOI: 10.1016/j.bbagen.2018.01.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 11/14/2017] [Accepted: 01/11/2018] [Indexed: 11/24/2022]
Abstract
BACKGROUND Golgi Reassembly and Stacking Proteins (GRASPs) are widely spread among eukaryotic cells (except plants) and are considered as key components in both the stacking of the Golgi cisternae and its lateral connection. Furthermore, GRASPs were also proved essential in the unconventional secretion pathway of several proteins, even though the mechanism remains obscure. It was previously observed that the GRASP homologue in Cryptococcus neoformans has a molten globule-like behavior in solution. METHODS We used circular dichroism, synchrotron radiation circular dichroism and steady-state as well as time-resolved fluorescence. RESULTS We report the disorder-to-order transition propensities for a native molten globule-like protein in the presence of different mimetics of cell conditions. Changes in the dielectric constant (such as those experienced close to the membrane surface) seem to be the major factor in inducing multiple disorder-to-order transitions in GRASP, which shows very distinct behavior when in conditions that mimic the vicinity of the membrane surface as compared to those found when free in solution. Other folding factors such as molecular crowding, counter ions, pH and phosphorylation exhibit lower or no effect on GRASP secondary structure and/or stability. GENERAL SIGNIFICANCE To the best of our knowledge, this is the first study focusing on understanding the disorder-to-order transitions of a molten globule structure without the need of any mild denaturing condition. A model is also introduced aiming at describing how the cell could manipulate the GRASP sensitivity to changes in the dielectric constant during different cell-cycle periods.
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Affiliation(s)
- Luís F S Mendes
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Luis G M Basso
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Patricia S Kumagai
- Grupo de Biofísica Molecular "Sérgio Mascarenhas", Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, SP, Brazil
| | - Raquel Fonseca-Maldonado
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil; Instituto Federal de São Paulo, Campus Jacareí, SP, Brazil
| | - Antonio J Costa-Filho
- Laboratório de Biofísica Molecular, Departamento de Física, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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Acharya N, Mishra P, Jha SK. A dry molten globule-like intermediate during the base-induced unfolding of a multidomain protein. Phys Chem Chem Phys 2017; 19:30207-30216. [DOI: 10.1039/c7cp06614g] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An early intermediate during the base-induced unfolding of a multidomain protein resembles a dry molten globule state in which the structure is expanded without core hydration.
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Affiliation(s)
- Nirbhik Acharya
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Prajna Mishra
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
| | - Santosh Kumar Jha
- Physical and Materials Chemistry Division
- CSIR-National Chemical Laboratory
- Pune 411008
- India
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Jones CR, Greenhalgh MD, Bame JR, Simpson TJ, Cox RJ, Marshall JW, Butts CP. Subtle temperature-induced changes in small molecule conformer dynamics – observed and quantified by NOE spectroscopy. Chem Commun (Camb) 2016; 52:2920-3. [DOI: 10.1039/c5cc10509a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
NOE–distance relationships are shown to be sufficiently accurate to monitor very small changes in conformer populations in response to temperature (<0.5%/10 °C) – in good agreement with Boltzmann-predictions.
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Affiliation(s)
- C. R. Jones
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
| | - M. D. Greenhalgh
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
| | - J. R. Bame
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
| | - T. J. Simpson
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
| | - R. J. Cox
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
- Leibniz Universität Hannover
| | - J. W. Marshall
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
| | - C. P. Butts
- School of Chemistry
- University of Bristol Cantocks Close
- Bristol
- UK
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Sales AE, Breydo L, Porto TS, Porto ALF, Uversky VN. Hydrophobicity-dependent effects of polymers on different protein conformations. RSC Adv 2016. [DOI: 10.1039/c6ra07910e] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Polymers can either induce or disrupt secondary and tertiary structure in partially disordered protein conformations. The balance of the forces driving these structural changes depends on the polymer hydrophobicity and protein sequence and structure.
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Affiliation(s)
- Amanda E. Sales
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Leonid Breydo
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
| | - Tatiana S. Porto
- Academic Unit of Garanhuns
- Federal Rural University of Pernambuco
- Garanhuns
- Brazil
| | - Ana L. F. Porto
- Department of Morphology and Animal Physiology
- Federal Rural University of Pernambuco
- 52171-900 Recife
- Brazil
| | - Vladimir N. Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute
- Morsani College of Medicine
- University of South Florida
- Tampa
- USA
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NMR as a tool to identify and characterize protein folding intermediates. Arch Biochem Biophys 2013; 531:90-9. [DOI: 10.1016/j.abb.2012.09.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2012] [Revised: 09/03/2012] [Accepted: 09/04/2012] [Indexed: 11/20/2022]
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Jaremko M, Jaremko Ł, Kim HY, Cho MK, Schwieters CD, Giller K, Becker S, Zweckstetter M. Cold denaturation of a protein dimer monitored at atomic resolution. Nat Chem Biol 2013; 9:264-70. [PMID: 23396077 DOI: 10.1038/nchembio.1181] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Accepted: 01/15/2013] [Indexed: 11/09/2022]
Abstract
Protein folding and unfolding are crucial for a range of biological phenomena and human diseases. Defining the structural properties of the involved transient species is therefore of prime interest. Using a combination of cold denaturation with NMR spectroscopy, we reveal detailed insight into the unfolding of the homodimeric repressor protein CylR2. Seven three-dimensional structures of CylR2 at temperatures from 25 °C to -16 °C reveal a progressive dissociation of the dimeric protein into a native-like monomeric intermediate followed by transition into a highly dynamic, partially folded state. The core of the partially folded state seems critical for biological function and misfolding.
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Affiliation(s)
- Mariusz Jaremko
- Department for NMR-based Structural Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
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Bhattacharyya S, Varadarajan R. Packing in molten globules and native states. Curr Opin Struct Biol 2012; 23:11-21. [PMID: 23270864 DOI: 10.1016/j.sbi.2012.10.010] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2012] [Accepted: 10/31/2012] [Indexed: 11/26/2022]
Abstract
Close packing of hydrophobic residues in the protein interior is an important determinant of protein stability. Cavities introduced by large to small substitutions are known to destabilize proteins. Conversely, native states of proteins and protein fragments can be stabilized by filling in existing cavities. Molten globules (MGs) were initially used to describe a state of protein which has well-defined secondary structure but little or no tertiary packing. Subsequent studies have shown that MGs do have some degree of native-like topology and specific packing. Wet molten globules (WMGs) with hydrated cores and considerably decreased packing relative to the native state have been studied extensively. Recently there has been renewed interest in identification and characterization of dry molten globules (DMGs). These are slightly expanded forms of the native state which show increased conformational flexibility, native-like main-chain hydrogen bonding and dry interiors. The generality of occurrence of DMGs during protein unfolding and the extent and nature of packing in DMGs remain to be elucidated. Packing interactions in native proteins and MGs can be probed through mutations. Next generation sequencing technologies make it possible to determine relative populations of mutants in a large pool. When this is coupled to phenotypic screens or cell-surface display, it becomes possible to rapidly examine large panels of single-site or multi-site mutants. From such studies, residue specific contributions to protein stability and function can be estimated in a highly parallelized fashion. This complements conventional biophysical methods for characterization of packing in native states and molten globules.
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Kovermann M, Zierold R, Haupt C, Löw C, Balbach J. NMR relaxation unravels interdomain crosstalk of the two domain prolyl isomerase and chaperone SlyD. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:873-81. [DOI: 10.1016/j.bbapap.2011.03.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 03/18/2011] [Accepted: 03/25/2011] [Indexed: 11/26/2022]
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Varshney A, Ahmad B, Rabbani G, Kumar V, Yadav S, Khan RH. Acid-induced unfolding of didecameric keyhole limpet hemocyanin: detection and characterizations of decameric and tetrameric intermediate states. Amino Acids 2010; 39:899-910. [DOI: 10.1007/s00726-010-0524-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Accepted: 02/10/2010] [Indexed: 10/19/2022]
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Kamau SM, Cheison SC, Chen W, Liu XM, Lu RR. Alpha-Lactalbumin: Its Production Technologies and Bioactive Peptides. Compr Rev Food Sci Food Saf 2010. [DOI: 10.1111/j.1541-4337.2009.00100.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Pettersson-Kastberg J, Mossberg AK, Trulsson M, Yong YJ, Min S, Lim Y, O'Brien JE, Svanborg C, Mok KH. α-Lactalbumin, Engineered to be Nonnative and Inactive, Kills Tumor Cells when in Complex with Oleic Acid: A New Biological Function Resulting from Partial Unfolding. J Mol Biol 2009; 394:994-1010. [DOI: 10.1016/j.jmb.2009.09.026] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2009] [Revised: 08/18/2009] [Accepted: 09/14/2009] [Indexed: 11/28/2022]
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Liu Z, Zhang J, Wang X, Ding Y, Wu J, Shi Y. Temperature-induced partially unfolded state of hUBF HMG Box-5: Conformational and dynamic investigations of the Box-5 thermal intermediate ensemble. Proteins 2009; 77:432-47. [DOI: 10.1002/prot.22454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Higman VA, Rösner HI, Ugolini R, Greene LH, Redfield C, Smith LJ. Probing the urea dependence of residual structure in denatured human alpha-lactalbumin. JOURNAL OF BIOMOLECULAR NMR 2009; 45:121-31. [PMID: 19618277 PMCID: PMC2728226 DOI: 10.1007/s10858-009-9342-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2009] [Accepted: 06/12/2009] [Indexed: 05/19/2023]
Abstract
Backbone (15)N relaxation parameters and (15)N-(1)H(N) residual dipolar couplings (RDCs) have been measured for a variant of human alpha-lactalbumin (alpha-LA) in 4, 6, 8 and 10 M urea. In the alpha-LA variant, the eight cysteine residues in the protein have been replaced by alanines (all-Ala alpha-LA). This protein is a partially folded molten globule at pH 2 and has been shown previously to unfold in a stepwise non-cooperative manner on the addition of urea. (15)N R(2) values in some regions of all-Ala alpha-LA show significant exchange broadening which is reduced as the urea concentration is increased. Experimental RDC data are compared with RDCs predicted from a statistical coil model and with bulkiness, average area buried upon folding and hydrophobicity profiles in order to identify regions of non-random structure. Residues in the regions corresponding to the B, D and C-terminal 3(10) helices in native alpha-LA show R(2) values and RDC data consistent with some non-random structural propensities even at high urea concentrations. Indeed, for residues 101-106 the residual structure persists in 10 M urea and the RDC data suggest that this might include the formation of a turn-like structure. The data presented here allow a detailed characterization of the non-cooperative unfolding of all-Ala alpha-LA at higher concentrations of denaturant and complement previous studies which focused on structural features of the molten globule which is populated at lower concentrations of denaturant.
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Affiliation(s)
- Victoria A. Higman
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
- Leibniz-Institut für Molekulare Pharmakologie, Robert-Rösle-Str. 10, Berlin, Germany
| | - Heike I. Rösner
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen, Denmark
| | - Raffaella Ugolini
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
| | - Lesley H. Greene
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
- Department of Chemistry and Biochemistry, Old Dominion University, 4541 Hampton Blvd., Norfolk, VA 23529-0126 USA
| | - Christina Redfield
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, UK
| | - Lorna J. Smith
- Department of Chemistry, Inorganic Chemistry Laboratory, University of Oxford, South Parks Road, Oxford, UK
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Bruylants G, Redfield C. (15)N NMR relaxation data reveal significant chemical exchange broadening in the alpha-domain of human alpha-lactalbumin. Biochemistry 2009; 48:4031-9. [PMID: 19309110 DOI: 10.1021/bi900023m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Human alpha-lactalbumin (alpha-LA), a 123-residue calcium-binding protein, has been studied using (15)N NMR relaxation methods in order to characterize backbone dynamics of the native state at the level of individual residues. Relaxation data were collected at three magnetic field strengths and analyzed using the model-free formalism of Lipari and Szabo. The order parameters derived from this analysis are generally high, indicating a rigid backbone. A total of 46 residues required an exchange contribution to T(2); 43 of these residues are located in the alpha-domain of the protein. The largest exchange contributions are observed in the A-, B-, D-, and C-terminal 3(10)-helices of the alpha-domain; these residues have been shown previously to form a highly stable core in the alpha-LA molten globule. The observed exchange broadening, along with previous hydrogen/deuterium amide exchange data, suggests that this part of the alpha-domain may undergo a local structural transition between the well-ordered native structure and a less-ordered molten-globule-like structure.
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Affiliation(s)
- Gilles Bruylants
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, United Kingdom
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