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Vergara R, Berrocal T, Juárez Mejía EI, Romero-Romero S, Velázquez-López I, Pulido NO, López Sanchez HA, Silva DA, Costas M, Rodríguez-Romero A, Rodríguez-Sotres R, Sosa-Peinado A, Fernández-Velasco DA. Thermodynamic and kinetic analysis of the LAO binding protein and its isolated domains reveal non-additivity in stability, folding and function. FEBS J 2023; 290:4496-4512. [PMID: 37178351 DOI: 10.1111/febs.16819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 05/12/2023] [Indexed: 05/15/2023]
Abstract
Substrate-binding proteins (SBPs) are used by organisms from the three domains of life for transport and signalling. SBPs are composed of two domains that collectively trap ligands with high affinity and selectivity. To explore the role of the domains and the integrity of the hinge region between them in the function and conformation of SBPs, here, we describe the ligand binding, conformational stability and folding kinetics of the Lysine Arginine Ornithine (LAO) binding protein from Salmonella thiphimurium and constructs corresponding to its two independent domains. LAO is a class II SBP formed by a continuous and a discontinuous domain. Contrary to the expected behaviour based on their connectivity, the discontinuous domain shows a stable native-like structure that binds l-arginine with moderate affinity, whereas the continuous domain is barely stable and shows no detectable ligand binding. Regarding folding kinetics, studies of the entire protein revealed the presence of at least two intermediates. While the unfolding and refolding of the continuous domain exhibited only a single intermediate and simpler and faster kinetics than LAO, the folding mechanism of the discontinuous domain was complex and involved multiple intermediates. These findings suggest that in the complete protein the continuous domain nucleates folding and that its presence funnels the folding of the discontinuous domain avoiding nonproductive interactions. The strong dependence of the function, stability and folding pathway of the lobes on their covalent association is most likely the result of the coevolution of both domains as a single unit.
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Affiliation(s)
- Renan Vergara
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Tania Berrocal
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Eva Isela Juárez Mejía
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Sergio Romero-Romero
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Department of Biochemistry, University of Bayreuth, Germany
| | - Isabel Velázquez-López
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Nancy O Pulido
- Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - Haven A López Sanchez
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Daniel-Adriano Silva
- Department of Biochemistry, University of Washington, Seattle, WA, USA
- Institute for Protein Design, University of Washington, Seattle, WA, USA
| | - Miguel Costas
- Laboratorio de Biofisicoquímica, Departamento de Fisicoquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | | | - Rogelio Rodríguez-Sotres
- Departamento de Bioquímica, Facultad de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Alejandro Sosa-Peinado
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - D Alejandro Fernández-Velasco
- Laboratorio de Fisicoquímica e Ingeniería de Proteínas, Departamento de Bioquímica, Facultad de Medicina, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
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Wang CK, Craik DJ. Linking molecular evolution to molecular grafting. J Biol Chem 2021; 296:100425. [PMID: 33600801 PMCID: PMC8005815 DOI: 10.1016/j.jbc.2021.100425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/09/2021] [Accepted: 02/13/2021] [Indexed: 12/01/2022] Open
Abstract
Molecular grafting is a strategy for the engineering of molecular scaffolds into new functional agents, such as next-generation therapeutics. Despite its wide use, studies so far have focused almost exclusively on demonstrating its utility rather than understanding the factors that lead to either poor or successful grafting outcomes. Here, we examine protein evolution and identify parallels between the natural process of protein functional diversification and the artificial process of molecular grafting. We discuss features of natural proteins that are correlated to innovability-the capacity to acquire new functions-and describe their implications to molecular grafting scaffolds. Disulfide-rich peptides are used as exemplars because they are particularly promising scaffolds onto which new functions can be grafted. This article provides a perspective on why some scaffolds are more suitable for grafting than others, identifying opportunities on how molecular grafting might be improved.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia.
| | - David J Craik
- Institute for Molecular Bioscience and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, Queensland, Australia
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Kuwajima K. The Molten Globule, and Two-State vs. Non-Two-State Folding of Globular Proteins. Biomolecules 2020; 10:biom10030407. [PMID: 32155758 PMCID: PMC7175247 DOI: 10.3390/biom10030407] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 03/03/2020] [Accepted: 03/06/2020] [Indexed: 11/16/2022] Open
Abstract
From experimental studies of protein folding, it is now clear that there are two types of folding behavior, i.e., two-state folding and non-two-state folding, and understanding the relationships between these apparently different folding behaviors is essential for fully elucidating the molecular mechanisms of protein folding. This article describes how the presence of the two types of folding behavior has been confirmed experimentally, and discusses the relationships between the two-state and the non-two-state folding reactions, on the basis of available data on the correlations of the folding rate constant with various structure-based properties, which are determined primarily by the backbone topology of proteins. Finally, a two-stage hierarchical model is proposed as a general mechanism of protein folding. In this model, protein folding occurs in a hierarchical manner, reflecting the hierarchy of the native three-dimensional structure, as embodied in the case of non-two-state folding with an accumulation of the molten globule state as a folding intermediate. The two-state folding is thus merely a simplified version of the hierarchical folding caused either by an alteration in the rate-limiting step of folding or by destabilization of the intermediate.
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Affiliation(s)
- Kunihiro Kuwajima
- Department of Physics, School of Science, the University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; ; Tel.: +81-90-5435-6540
- School of Computational Sciences, Korea Institute for Advanced Study (KIAS), Seoul 02455, Korea
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Surana P, Das R. Observing a late folding intermediate of Ubiquitin at atomic resolution by NMR. Protein Sci 2016; 25:1438-50. [PMID: 27111887 DOI: 10.1002/pro.2940] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 04/20/2016] [Indexed: 01/29/2023]
Abstract
The study of intermediates in the protein folding pathway provides a wealth of information about the energy landscape. The intermediates also frequently initiate pathogenic fibril formations. While observing the intermediates is difficult due to their transient nature, extreme conditions can partially unfold the proteins and provide a glimpse of the intermediate states. Here, we observe the high resolution structure of a hydrophobic core mutant of Ubiquitin at an extreme acidic pH by nuclear magnetic resonance (NMR) spectroscopy. In the structure, the native secondary and tertiary structure is conserved for a major part of the protein. However, a long loop between the beta strands β3 and β5 is partially unfolded. The altered structure is supported by fluorescence data and the difference in free energies between the native state and the intermediate is reflected in the denaturant induced melting curves. The unfolded region includes amino acids that are critical for interaction with cofactors as well as for assembly of poly-Ubiquitin chains. The structure at acidic pH resembles a late folding intermediate of Ubiquitin and indicates that upon stabilization of the protein's core, the long loop converges on the core in the final step of the folding process.
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Affiliation(s)
- Parag Surana
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
| | - Ranabir Das
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bengaluru, 560065, Karnataka, India
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Mahapa A, Mandal S, Biswas A, Jana B, Polley S, Sau S, Sau K. Chemical and thermal unfolding of a global staphylococcal virulence regulator with a flexible C-terminal end. PLoS One 2015; 10:e0122168. [PMID: 25822635 PMCID: PMC4379015 DOI: 10.1371/journal.pone.0122168] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 02/07/2015] [Indexed: 11/19/2022] Open
Abstract
SarA, a Staphylococcus aureus-specific dimeric protein, modulates the expression of numerous proteins including various virulence factors. Interestingly, S. aureus synthesizes multiple SarA paralogs seemingly for optimizing the expression of its virulence factors. To understand the domain structure/flexibility and the folding/unfolding mechanism of the SarA protein family, we have studied a recombinant SarA (designated rSarA) using various in vitro probes. Limited proteolysis of rSarA and the subsequent analysis of the resulting protein fragments suggested it to be a single-domain protein with a long, flexible C-terminal end. rSarA was unfolded by different mechanisms in the presence of different chemical and physical denaturants. While urea-induced unfolding of rSarA occurred successively via the formation of a dimeric and a monomeric intermediate, GdnCl-induced unfolding of this protein proceeded through the production of two dimeric intermediates. The surface hydrophobicity and the structures of the intermediates were not identical and also differed significantly from those of native rSarA. Of the intermediates, the GdnCl-generated intermediates not only possessed a molten globule-like structure but also exhibited resistance to dissociation during their unfolding. Compared to the native rSarA, the intermediate that was originated at lower GdnCl concentration carried a compact shape, whereas, other intermediates owned a swelled shape. The chemical-induced unfolding, unlike thermal unfolding of rSarA, was completely reversible in nature.
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Affiliation(s)
- Avisek Mahapa
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
| | - Sukhendu Mandal
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Anindya Biswas
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Biswanath Jana
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Soumitra Polley
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
| | - Subrata Sau
- Department of Biochemistry, Bose Institute, Kolkata, West Bengal, India
- * E-mail: (SS); (KS)
| | - Keya Sau
- Department of Biotechnology, Haldia Institute of Technology, Haldia, West Bengal, India
- * E-mail: (SS); (KS)
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6
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Kister A. Amino acid distribution rules predict protein fold: protein grammar for beta-strand sandwich-like structures. Biomolecules 2015; 5:41-59. [PMID: 25625198 PMCID: PMC4384110 DOI: 10.3390/biom5010041] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Accepted: 12/31/2014] [Indexed: 11/16/2022] Open
Abstract
We present an alternative approach to protein 3D folding prediction based on determination of rules that specify distribution of "favorable" residues, that are mainly responsible for a given fold formation, and "unfavorable" residues, that are incompatible with that fold, in polypeptide sequences. The process of determining favorable and unfavorable residues is iterative. The starting assumptions are based on the general principles of protein structure formation as well as structural features peculiar to a protein fold under investigation. The initial assumptions are tested one-by-one for a set of all known proteins with a given structure. The assumption is accepted as a "rule of amino acid distribution" for the protein fold if it holds true for all, or near all, structures. If the assumption is not accepted as a rule, it can be modified to better fit the data and then tested again in the next step of the iterative search algorithm, or rejected. We determined the set of amino acid distribution rules for a large group of beta sandwich-like proteins characterized by a specific arrangement of strands in two beta sheets. It was shown that this set of rules is highly sensitive (~90%) and very specific (~99%) for identifying sequences of proteins with specified beta sandwich fold structure. The advantage of the proposed approach is that it does not require that query proteins have a high degree of homology to proteins with known structure. So long as the query protein satisfies residue distribution rules, it can be confidently assigned to its respective protein fold. Another advantage of our approach is that it allows for a better understanding of which residues play an essential role in protein fold formation. It may, therefore, facilitate rational protein engineering design.
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Affiliation(s)
- Alexander Kister
- Department of Mathematics, Rutgers University, Piscataway, NJ 08854, USA.
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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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Savinov A, Perez CF, Block SM. Single-molecule studies of riboswitch folding. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2014; 1839:1030-1045. [PMID: 24727093 DOI: 10.1016/j.bbagrm.2014.04.005] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/27/2014] [Accepted: 04/03/2014] [Indexed: 10/25/2022]
Abstract
The folding dynamics of riboswitches are central to their ability to modulate gene expression in response to environmental cues. In most cases, a structural competition between the formation of a ligand-binding aptamer and an expression platform (or some other competing off-state) determines the regulatory outcome. Here, we review single-molecule studies of riboswitch folding and function, predominantly carried out using single-molecule FRET or optical trapping approaches. Recent results have supplied new insights into riboswitch folding energy landscapes, the mechanisms of ligand binding, the roles played by divalent ions, the applicability of hierarchical folding models, and kinetic vs. thermodynamic control schemes. We anticipate that future work, based on improved data sets and potentially combining multiple experimental techniques, will enable the development of more complete models for complex RNA folding processes. This article is part of a Special Issue entitled: Riboswitches.
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Affiliation(s)
- Andrew Savinov
- Biophysics Program, Stanford University, Stanford, CA 94305, USA
| | | | - Steven M Block
- Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA.
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Mabbitt PD, Eaton-Rye JJ, Wilbanks SM. Mutational analysis of the stability of Psb27 from Synechocystis sp. PCC 6803: implications for models of Psb27 structure and binding to CP43. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:787-93. [DOI: 10.1007/s00249-013-0926-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Revised: 07/27/2013] [Accepted: 08/20/2013] [Indexed: 11/28/2022]
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