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Vincenzi M, Mercurio FA, Leone M. NMR Spectroscopy in the Conformational Analysis of Peptides: An Overview. Curr Med Chem 2021; 28:2729-2782. [PMID: 32614739 DOI: 10.2174/0929867327666200702131032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 05/21/2020] [Accepted: 05/28/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND NMR spectroscopy is one of the most powerful tools to study the structure and interaction properties of peptides and proteins from a dynamic perspective. Knowing the bioactive conformations of peptides is crucial in the drug discovery field to design more efficient analogue ligands and inhibitors of protein-protein interactions targeting therapeutically relevant systems. OBJECTIVE This review provides a toolkit to investigate peptide conformational properties by NMR. METHODS Articles cited herein, related to NMR studies of peptides and proteins were mainly searched through PubMed and the web. More recent and old books on NMR spectroscopy written by eminent scientists in the field were consulted as well. RESULTS The review is mainly focused on NMR tools to gain the 3D structure of small unlabeled peptides. It is more application-oriented as it is beyond its goal to deliver a profound theoretical background. However, the basic principles of 2D homonuclear and heteronuclear experiments are briefly described. Protocols to obtain isotopically labeled peptides and principal triple resonance experiments needed to study them, are discussed as well. CONCLUSION NMR is a leading technique in the study of conformational preferences of small flexible peptides whose structure can be often only described by an ensemble of conformations. Although NMR studies of peptides can be easily and fast performed by canonical protocols established a few decades ago, more recently we have assisted to tremendous improvements of NMR spectroscopy to investigate instead large systems and overcome its molecular weight limit.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Flavia Anna Mercurio
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council of Italy, Via Mezzocannone 16, 80134, Naples, Italy
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Rosú SA, Rimoldi OJ, Prieto ED, Curto LM, Delfino JM, Ramella NA, Tricerri MA. Amyloidogenic propensity of a natural variant of human apolipoprotein A-I: stability and interaction with ligands. PLoS One 2015; 10:e0124946. [PMID: 25950566 PMCID: PMC4423886 DOI: 10.1371/journal.pone.0124946] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 03/19/2015] [Indexed: 12/18/2022] Open
Abstract
A number of naturally occurring mutations of human apolipoprotein A-I (apoA-I) have been associated with hereditary amyloidoses. The molecular mechanisms involved in amyloid-associated pathology remain largely unknown. Here we examined the effects of the Arg173Pro point mutation in apoA-I on the structure, stability, and aggregation propensity, as well as on the ability to bind to putative ligands. Our results indicate that the mutation induces a drastic loss of stability, and a lower efficiency to bind to phospholipid vesicles at physiological pH, which could determine the observed higher tendency to aggregate as pro-amyloidogenic complexes. Incubation under acidic conditions does not seem to induce significant desestabilization or aggregation tendency, neither does it contribute to the binding of the mutant to sodium dodecyl sulfate. While the binding to this detergent is higher for the mutant as compared to wt apoA-I, the interaction of the Arg173Pro variant with heparin depends on pH, being lower at pH 5.0 and higher than wt under physiological pH conditions. We suggest that binding to ligands as heparin or other glycosaminoglycans could be key events tuning the fine details of the interaction of apoA-I variants with the micro-environment, and probably eliciting the toxicity of these variants in hereditary amyloidoses.
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Affiliation(s)
- Silvana A. Rosú
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Omar J. Rimoldi
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - Eduardo D. Prieto
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA), Universidad Nacional de La Plata-CONICET, La Plata, Buenos Aires, Argentina
| | - Lucrecia M. Curto
- Departamento de Química Biológica e Instituto de Bioquímica y Biofísica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - José M. Delfino
- Departamento de Química Biológica e Instituto de Bioquímica y Biofísica, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nahuel A. Ramella
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
| | - M. Alejandra Tricerri
- Instituto de Investigaciones Bioquímicas de La Plata (INIBIOLP), CONICET, La Plata, Buenos Aires, Argentina
- Facultad de Ciencias Médicas, Universidad Nacional de La Plata, La Plata, Buenos Aires, Argentina
- * E-mail:
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Vazquez DS, Sánchez IE, Garrote A, Sica MP, Santos J. The E. coli thioredoxin folding mechanism: The key role of the C-terminal helix. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2015; 1854:127-37. [DOI: 10.1016/j.bbapap.2014.11.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2014] [Revised: 10/23/2014] [Accepted: 11/10/2014] [Indexed: 10/24/2022]
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Vazquez DS, Agudelo WA, Yone A, Vizioli N, Arán M, González Flecha FL, González Lebrero MC, Santos J. A helix–coil transition induced by the metal ion interaction with a grafted iron-binding site of the CyaY protein family. Dalton Trans 2015; 44:2370-9. [DOI: 10.1039/c4dt02796e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An iron-binding motif EExxED from the first α-helical stretch of frataxin was grafted on a foreign peptide scaffold:KD= 1.9 ± 0.2 μM and 1 : 1 stoichiometry.
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Affiliation(s)
- Diego S. Vazquez
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - William A. Agudelo
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Angel Yone
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Nora Vizioli
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Martín Arán
- Fundación Instituto Leloir and IIBBA – CONICET
- 1405 Buenos Aires
- Argentina
| | - F. Luis González Flecha
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Mariano C. González Lebrero
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
| | - Javier Santos
- Instituto de Química y Físico – Química Biológicas
- Universidad de Buenos Aires – CONICET
- Buenos Aires
- Argentina
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5
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Zaidi N, Nusrat S, Zaidi FK, Khan RH. pH-Dependent Differential Interacting Mechanisms of Sodium Dodecyl Sulfate with Bovine Serum Fetuin: A Biophysical Insight. J Phys Chem B 2014; 118:13025-36. [DOI: 10.1021/jp501515g] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nida Zaidi
- Interdisciplinary Biotechnology
Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Saima Nusrat
- Interdisciplinary Biotechnology
Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Fatima Kamal Zaidi
- Interdisciplinary Biotechnology
Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan H. Khan
- Interdisciplinary Biotechnology
Unit, Aligarh Muslim University, Aligarh 202002, India
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Roman EA, González Flecha FL. Kinetics and thermodynamics of membrane protein folding. Biomolecules 2014; 4:354-73. [PMID: 24970219 PMCID: PMC4030980 DOI: 10.3390/biom4010354] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Revised: 02/19/2014] [Accepted: 02/23/2014] [Indexed: 02/06/2023] Open
Abstract
Understanding protein folding has been one of the great challenges in biochemistry and molecular biophysics. Over the past 50 years, many thermodynamic and kinetic studies have been performed addressing the stability of globular proteins. In comparison, advances in the membrane protein folding field lag far behind. Although membrane proteins constitute about a third of the proteins encoded in known genomes, stability studies on membrane proteins have been impaired due to experimental limitations. Furthermore, no systematic experimental strategies are available for folding these biomolecules in vitro. Common denaturing agents such as chaotropes usually do not work on helical membrane proteins, and ionic detergents have been successful denaturants only in few cases. Refolding a membrane protein seems to be a craftsman work, which is relatively straightforward for transmembrane β-barrel proteins but challenging for α-helical membrane proteins. Additional complexities emerge in multidomain membrane proteins, data interpretation being one of the most critical. In this review, we will describe some recent efforts in understanding the folding mechanism of membrane proteins that have been reversibly refolded allowing both thermodynamic and kinetic analysis. This information will be discussed in the context of current paradigms in the protein folding field.
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Affiliation(s)
- Ernesto A Roman
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
| | - F Luis González Flecha
- Laboratory of Molecular Biophysics, Institute of Biochemistry and Biophysical Chemistry, University of Buenos Aires-CONICET, Buenos Aires 1113, Argentina.
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Iannucci NB, Curto LM, Albericio F, Cascone O, Delfino JM. Structural glance into a novel anti-staphylococcal peptide. Biopolymers 2014; 102:49-57. [DOI: 10.1002/bip.22394] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 07/20/2013] [Accepted: 07/24/2013] [Indexed: 11/11/2022]
Affiliation(s)
- N. B. Iannucci
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
- Therapeutic Peptides Research and Development Laboratory; Chemo-Romikin, Carlos Villate 5148, B1605AXL, Buenos Aires; Argentina
| | - L. M. Curto
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
| | - F. Albericio
- Institute for Research in Biomedicine; Barcelona Science Park, c/Baldiri Reixac 10, 08028; Barcelona, Spain
- CIBER-BBN, Networking Centre on Bioengineering; Biomaterials and Nanomedicine, Barcelona Science Park, c/Baldiri Reixac 10, 08028; Barcelona, Spain
- Department of Organic Chemistry, School of Chemistry; University of Barcelona, Martí i Franquès 1-11, 08028; Barcelona, Spain
- School of Chemistry and Physics; University of KwaZulu-Natal; Westville Campus, University Road, Westville, 4001-Durban South Africa
| | - O. Cascone
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
| | - J. M. Delfino
- Department of Biological Chemistry and Institute of Biochemistry and Biophysics (IQUIFIB), School of Pharmacy and Biochemistry; University of Buenos Aires; Junín 956, C1113AAD Buenos Aires, Argentina
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The role of the N-terminal tail for the oligomerization, folding and stability of human frataxin. FEBS Open Bio 2013; 3:310-20. [PMID: 23951553 PMCID: PMC3741918 DOI: 10.1016/j.fob.2013.07.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 07/10/2013] [Accepted: 07/15/2013] [Indexed: 01/30/2023] Open
Abstract
The N-terminal stretch of human frataxin (hFXN) intermediate (residues 42–80) is not conserved throughout evolution and, under defined experimental conditions, behaves as a random-coil. Overexpression of hFXN56–210 in Escherichia coli yields a multimer, whereas the mature form of hFXN (hFXN81–210) is monomeric. Thus, cumulative experimental evidence points to the N-terminal moiety as an essential element for the assembly of a high molecular weight oligomer. The secondary structure propensity of peptide 56–81, the moiety putatively responsible for promoting protein–protein interactions, was also studied. Depending on the environment (TFE or SDS), this peptide adopts α-helical or β-strand structure. In this context, we explored the conformation and stability of hFXN56–210. The biophysical characterization by fluorescence, CD and SEC-FPLC shows that subunits are well folded, sharing similar stability to hFXN90–210. However, controlled proteolysis indicates that the N-terminal stretch is labile in the context of the multimer, whereas the FXN domain (residues 81–210) remains strongly resistant. In addition, guanidine hydrochloride at low concentration disrupts intermolecular interactions, shifting the ensemble toward the monomeric form. The conformational plasticity of the N-terminal tail might impart on hFXN the ability to act as a recognition signal as well as an oligomerization trigger. Understanding the fine-tuning of these activities and their resulting balance will bear direct relevance for ultimately comprehending hFXN function. hFXN56–210 is well-folded and shares similar stability to hFXN90–210. The oligomeric form of hFXN56–210 can be disassembled and reassembled in vitro. Proteolysis leads to the oligomer disassembly: subunits are abridged to hFXN81–210. Isolated peptide hFXN56–81 acquires structure in TFE and SDS solutions. The N-terminal tail is structurally malleable and triggers oligomerization.
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Roman EA, Faraj SE, Gallo M, Salvay AG, Ferreiro DU, Santos J. Protein stability and dynamics modulation: the case of human frataxin. PLoS One 2012; 7:e45743. [PMID: 23049850 PMCID: PMC3458073 DOI: 10.1371/journal.pone.0045743] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2012] [Accepted: 08/24/2012] [Indexed: 01/06/2023] Open
Abstract
Frataxin (FXN) is an α/β protein that plays an essential role in iron homeostasis. Apparently, the function of human FXN (hFXN) depends on the cooperative formation of crucial interactions between helix α1, helix α2, and the C-terminal region (CTR) of the protein. In this work we quantitatively explore these relationships using a purified recombinant fragment hFXN90-195. This variant shows the hydrodynamic behavior expected for a monomeric globular domain. Circular dichroism, fluorescence, and NMR spectroscopies show that hFXN90-195 presents native-like secondary and tertiary structure. However, chemical and temperature induced denaturation show that CTR truncation significantly destabilizes the overall hFXN fold. Accordingly, limited proteolysis experiments suggest that the native-state dynamics of hFXN90-195 and hFXN90-210 are indeed different, being the former form much more sensitive to the protease at specific sites. The overall folding dynamics of hFXN fold was further explored with structure-based protein folding simulations. These suggest that the native ensemble of hFXN can be decomposed in at least two substates, one with consolidation of the CTR and the other without consolidation of the CTR. Explicit-solvent all atom simulations identify some of the proteolytic target sites as flexible regions of the protein. We propose that the local unfolding of CTR may be a critical step for the global unfolding of hFXN, and that modulation of the CTR interactions may strongly affect hFXN physiological function.
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Affiliation(s)
- Ernesto A. Roman
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
- Protein Physiology Laboratory, Departamento de Química Biológica-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Santiago E. Faraj
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariana Gallo
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires, Argentina
| | - Andres G. Salvay
- Instituto de Física de Líquidos y Sistemas Biológicos, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, La Plata, Argentina
- Departamento de Ciencia y Tecnología, Universidad Nacional Quilmes, Bernal, Provincia de Buenos Aires, Argentina
| | - Diego U. Ferreiro
- Protein Physiology Laboratory, Departamento de Química Biológica-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Javier Santos
- Instituto de Química y Físico-Química Biológicas, Universidad de Buenos Aires, Buenos Aires, Argentina
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Binolfi A, Fernández CO, Sica MP, Delfino JM, Santos J. Recognition between a short unstructured peptide and a partially folded fragment leads to the thioredoxin fold sharing native-like dynamics. Proteins 2012; 80:1448-64. [DOI: 10.1002/prot.24043] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 12/27/2011] [Accepted: 01/11/2012] [Indexed: 11/09/2022]
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