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Okuno Y, Schwieters CD, Yang Z, Clore GM. Theory and Applications of Nitroxide-based Paramagnetic Cosolutes for Probing Intermolecular and Electrostatic Interactions on Protein Surfaces. J Am Chem Soc 2022; 144:21371-21388. [DOI: 10.1021/jacs.2c10035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yusuke Okuno
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Charles D. Schwieters
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
- Computational Biomolecular Magnetic Resonance Core, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
| | - Zhilin Yang
- Laboratory of Cell Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
| | - G. Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892-0520, United States
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2
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Lenard AJ, Mulder FAA, Madl T. Solvent paramagnetic relaxation enhancement as a versatile method for studying structure and dynamics of biomolecular systems. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2022; 132-133:113-139. [PMID: 36496256 DOI: 10.1016/j.pnmrs.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 09/14/2022] [Accepted: 09/15/2022] [Indexed: 06/17/2023]
Abstract
Solvent paramagnetic relaxation enhancement (sPRE) is a versatile nuclear magnetic resonance (NMR)-based method that allows characterization of the structure and dynamics of biomolecular systems through providing quantitative experimental information on solvent accessibility of NMR-active nuclei. Addition of soluble paramagnetic probes to the solution of a biomolecule leads to paramagnetic relaxation enhancement in a concentration-dependent manner. Here we review recent progress in the sPRE-based characterization of structural and dynamic properties of biomolecules and their complexes, and aim to deliver a comprehensive illustration of a growing number of applications of the method to various biological systems. We discuss the physical principles of sPRE measurements and provide an overview of available co-solute paramagnetic probes. We then explore how sPRE, in combination with complementary biophysical techniques, can further advance biomolecular structure determination, identification of interaction surfaces within protein complexes, and probing of conformational changes and low-population transient states, as well as deliver insights into weak, nonspecific, and transient interactions between proteins and co-solutes. In addition, we present examples of how the incorporation of solvent paramagnetic probes can improve the sensitivity of NMR experiments and discuss the prospects of applying sPRE to NMR metabolomics, drug discovery, and the study of intrinsically disordered proteins.
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Affiliation(s)
- Aneta J Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria.
| | - Frans A A Mulder
- Interdisciplinary Nanoscience Center and Department of Chemistry, University of Aarhus, DK-8000 Aarhus, Denmark; Institute of Biochemistry, Johannes Kepler Universität Linz, 4040 Linz, Austria.
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Ageing, Molecular Biology and Biochemistry, Research Unit Integrative Structural Biology, Medical University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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3
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Miao Q, Nitsche C, Orton H, Overhand M, Otting G, Ubbink M. Paramagnetic Chemical Probes for Studying Biological Macromolecules. Chem Rev 2022; 122:9571-9642. [PMID: 35084831 PMCID: PMC9136935 DOI: 10.1021/acs.chemrev.1c00708] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Indexed: 12/11/2022]
Abstract
Paramagnetic chemical probes have been used in electron paramagnetic resonance (EPR) and nuclear magnetic resonance (NMR) spectroscopy for more than four decades. Recent years witnessed a great increase in the variety of probes for the study of biological macromolecules (proteins, nucleic acids, and oligosaccharides). This Review aims to provide a comprehensive overview of the existing paramagnetic chemical probes, including chemical synthetic approaches, functional properties, and selected applications. Recent developments have seen, in particular, a rapid expansion of the range of lanthanoid probes with anisotropic magnetic susceptibilities for the generation of structural restraints based on residual dipolar couplings and pseudocontact shifts in solution and solid state NMR spectroscopy, mostly for protein studies. Also many new isotropic paramagnetic probes, suitable for NMR measurements of paramagnetic relaxation enhancements, as well as EPR spectroscopic studies (in particular double resonance techniques) have been developed and employed to investigate biological macromolecules. Notwithstanding the large number of reported probes, only few have found broad application and further development of probes for dedicated applications is foreseen.
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Affiliation(s)
- Qing Miao
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
- School
of Chemistry &Chemical Engineering, Shaanxi University of Science & Technology, Xi’an710021, China
| | - Christoph Nitsche
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Henry Orton
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Mark Overhand
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
| | - Gottfried Otting
- Research
School of Chemistry, The Australian National
University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
- ARC
Centre of Excellence for Innovations in Peptide & Protein Science,
Research School of Chemistry, Australian
National University, Sullivans Creek Road, Canberra, Australian Capital Territory 2601, Australia
| | - Marcellus Ubbink
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, Leiden 2333 CC, The Netherlands
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4
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Sequence-specific assignments in NMR spectra of paramagnetic systems: A non-systematic approach. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.119984] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Nepravishta R, Walpole S, Tailford L, Juge N, Angulo J. Deriving Ligand Orientation in Weak Protein-Ligand Complexes by DEEP-STD NMR Spectroscopy in the Absence of Protein Chemical-Shift Assignment. Chembiochem 2018; 20:340-344. [PMID: 30379391 PMCID: PMC6468252 DOI: 10.1002/cbic.201800568] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Indexed: 01/07/2023]
Abstract
Differential epitope mapping saturation transfer difference (DEEP‐STD) NMR spectroscopy is a recently developed powerful approach for elucidating the structure and pharmacophore of weak protein–ligand interactions, as it reports key information on the orientation of the ligand and the architecture of the binding pocket.1 The method relies on selective saturation of protein residues in the binding site and the generation of a differential epitope map by observing the ligand, which depicts the nature of the protein residues making contact with the ligand in the bound state. Selective saturation requires knowledge of the chemical‐shift assignment of the protein residues, which can be obtained either experimentally by NMR spectroscopy or predicted from 3D structures. Herein, we propose a simple experimental procedure to expand the DEEP‐STD NMR methodology to protein–ligand cases in which the spectral assignment of the protein is not available. This is achieved by experimentally identifying the chemical shifts of the residues present in binding hot‐spots on the surface of the receptor protein by using 2D NMR experiments combined with a paramagnetic probe.
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Affiliation(s)
- Ridvan Nepravishta
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Samuel Walpole
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
| | - Louise Tailford
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Nathalie Juge
- The Gut Microbes and Health Institute Strategic Program, Quadram Institute of Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UA, UK
| | - Jesus Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK
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6
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Niccolai N, Morandi E, Gardini S, Costabile V, Spadaccini R, Crescenzi O, Picone D, Spiga O, Bernini A. Hot spot mapping of protein surfaces with TEMPOL: Bovine pancreatic RNase A as a model system. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1865:201-207. [PMID: 27890678 DOI: 10.1016/j.bbapap.2016.11.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/03/2016] [Accepted: 11/22/2016] [Indexed: 10/20/2022]
Abstract
TEMPOL spin-label has been used to identify surface exposure of protein nuclei from NMR analysis of the induced paramagnetic relaxation enhancements (PRE). The absence of linear dependence between atom depths and observed PRE reveals that specific mechanisms drive the approach of the paramagnet to the protein surface. RNase A represents a unique protein system to explore the fine details of the information offered by TEMPOL induced PRE, due to the abundance of previous results, obtained in solution and in the crystal, dealing with surface dynamics behavior of this protein. MD simulations in explicit solvent have been performed, also in the presence of TEMPOL, in order to delineate the role of intermolecular hydrogen bonds (HB) on PRE extents. Comparison of our results with the ones obtained from multiple solvent crystal structure (MSCS) studies yields information on the specificities that these two techniques have for characterizing protein-ligand interactions, a fundamental step in the development of reliable surface druggability predictors.
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Affiliation(s)
- Neri Niccolai
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Edoardo Morandi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Simone Gardini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Valentino Costabile
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Roberta Spadaccini
- Dipartimento di Scienze e Tecnologie, Università del Sannio, Via Port'Arsa 11, 82100 Benevento, Italy.
| | - Orlando Crescenzi
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italy.
| | - Delia Picone
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli Federico II, Via Cintia, 80126 Napoli, Italy.
| | - Ottavia Spiga
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
| | - Andrea Bernini
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, Via A. Moro 2, 53100 Siena, Italy.
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7
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Alvares R, Gupta S, Macdonald PM, Prosser RS. Temperature and Pressure Based NMR Studies of Detergent Micelle Phase Equilibria. J Phys Chem B 2014; 118:5698-706. [DOI: 10.1021/jp500139p] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Rohan Alvares
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Shaan Gupta
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - Peter M. Macdonald
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
| | - R. Scott Prosser
- Department
of Chemistry, University of Toronto, UTM Campus, 3359 Mississauga
Road North, Mississauga, Ontario, Canada L5L 1C6
- Department
of Biochemistry, University of Toronto, Toronto, Ontario, Canada M5S 1A8
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8
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Bernini A, Henrici De Angelis L, Morandi E, Spiga O, Santucci A, Assfalg M, Molinari H, Pillozzi S, Arcangeli A, Niccolai N. Searching for protein binding sites from Molecular Dynamics simulations and paramagnetic fragment-based NMR studies. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1844:561-6. [PMID: 24373878 DOI: 10.1016/j.bbapap.2013.12.012] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 12/16/2013] [Accepted: 12/18/2013] [Indexed: 11/30/2022]
Abstract
Hotspot delineation on protein surfaces represents a fundamental step for targeting protein-protein interfaces. Disruptors of protein-protein interactions can be designed provided that the sterical features of binding pockets, including the transient ones, can be defined. Molecular Dynamics, MD, simulations have been used as a reliable framework for identifying transient pocket openings on the protein surface. Accessible surface area and intramolecular H-bond involvement of protein backbone amides are proposed as descriptors for characterizing binding pocket occurrence and evolution along MD trajectories. TEMPOL induced paramagnetic perturbations on (1)H-(15)N HSQC signals of protein backbone amides have been analyzed as a fragment-based search for surface hotspots, in order to validate MD predicted pockets. This procedure has been applied to CXCL12, a small chemokine responsible for tumor progression and proliferation. From combined analysis of MD data and paramagnetic profiles, two CXCL12 sites suitable for the binding of small molecules were identified. One of these sites is the already well characterized CXCL12 region involved in the binding to CXCR4 receptor. The other one is a transient pocket predicted by Molecular Dynamics simulations, which could not be observed from static analysis of CXCL12 PDB structures. The present results indicate how TEMPOL, instrumental in identifying this transient pocket, can be a powerful tool to delineate minor conformations which can be highly relevant in dynamic discovery of antitumoral drugs.
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Affiliation(s)
- Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | | | - Edoardo Morandi
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; SienaBioGrafiX Srl, 53100 Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Michael Assfalg
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | | | - Serena Pillozzi
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, 50134 Florence, Italy
| | - Annarosa Arcangeli
- Dipartimento di Medicina Sperimentale e Clinica, University of Florence, 50134 Florence, Italy
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy; SienaBioGrafiX Srl, 53100 Siena, Italy.
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9
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Hocking HG, Zangger K, Madl T. Studying the structure and dynamics of biomolecules by using soluble paramagnetic probes. Chemphyschem 2013; 14:3082-94. [PMID: 23836693 PMCID: PMC4171756 DOI: 10.1002/cphc.201300219] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Indexed: 12/20/2022]
Abstract
Characterisation of the structure and dynamics of large biomolecules and biomolecular complexes by NMR spectroscopy is hampered by increasing overlap and severe broadening of NMR signals. As a consequence, the number of available NMR spectroscopy data is often sparse and new approaches to provide complementary NMR spectroscopy data are needed. Paramagnetic relaxation enhancements (PREs) obtained from inert and soluble paramagnetic probes (solvent PREs) provide detailed quantitative information about the solvent accessibility of NMR-active nuclei. Solvent PREs can be easily measured without modification of the biomolecule; are sensitive to molecular structure and dynamics; and are therefore becoming increasingly powerful for the study of biomolecules, such as proteins, nucleic acids, ligands and their complexes in solution. In this Minireview, we give an overview of the available solvent PRE probes and discuss their applications for structural and dynamic characterisation of biomolecules and biomolecular complexes.
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Affiliation(s)
- Henry G Hocking
- Chair of Biomolecular NMR, Department Chemie, Technische Universität München, 85747 Garching (Germany); Institute of Structural Biology, Helmholtz Zentrum München, 85764 Neuherberg (Germany)
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10
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Solution NMR studies on the orientation of membrane-bound peptides and proteins by paramagnetic probes. Molecules 2013; 18:7407-35. [PMID: 23799448 PMCID: PMC6269851 DOI: 10.3390/molecules18077407] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2013] [Revised: 06/13/2013] [Accepted: 06/20/2013] [Indexed: 12/24/2022] Open
Abstract
Many peptides and proteins are attached to or immersed in a biological membrane. In order to understand their function not only the structure but also their topology in the membrane is important. Solution NMR spectroscopy is one of the most often used approaches to determine the orientation and localization of membrane-bound peptides and proteins. Here we give an application-oriented overview on the use of paramagnetic probes for the investigation of membrane-bound peptides and proteins. The examples discussed range from the large pool of antimicrobial peptides, bacterial toxins, cell penetrating peptides to domains of larger proteins or the calcium regulating protein phospholamban. Topological information is obtained in all these examples by the use of either attached or freely mobile paramagnetic tags. For some examples information obtained from the paramagnetic probes was included in the structure determination.
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Hohlweg W, Kosol S, Zangger K. Determining the orientation and localization of membrane-bound peptides. Curr Protein Pept Sci 2012; 13:267-79. [PMID: 22044140 PMCID: PMC3394173 DOI: 10.2174/138920312800785049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2010] [Revised: 10/01/2011] [Accepted: 10/10/2011] [Indexed: 01/06/2023]
Abstract
Many naturally occurring bioactive peptides bind to biological membranes. Studying and elucidating the mode of interaction is often an essential step to understand their molecular and biological functions. To obtain the complete orientation and immersion depth of such compounds in the membrane or a membrane-mimetic system, a number of methods are available, which are separated in this review into four main classes: solution NMR, solid-state NMR, EPR and other methods. Solution NMR methods include the Nuclear Overhauser Effect (NOE) between peptide and membrane signals, residual dipolar couplings and the use of paramagnetic probes, either within the membrane-mimetic or in the solvent. The vast array of solid state NMR methods to study membrane-bound peptide orientation and localization includes the anisotropic chemical shift, PISA wheels, dipolar waves, the GALA, MAOS and REDOR methods and again the use of paramagnetic additives on relaxation rates. Paramagnetic additives, with their effect on spectral linewidths, have also been used in EPR spectroscopy. Additionally, the orientation of a peptide within a membrane can be obtained by the anisotropic hyperfine tensor of a rigidly attached nitroxide label. Besides these magnetic resonance techniques a series of other methods to probe the orientation of peptides in membranes has been developed, consisting of fluorescence-, infrared- and oriented circular dichroism spectroscopy, colorimetry, interface-sensitive X-ray and neutron scattering and Quartz crystal microbalance.
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Affiliation(s)
| | | | - Klaus Zangger
- Institute of Chemistry / Organic and Bioorganic Chemistry, University of Graz, Heinrichstrasse 28, A-8010 Graz, Austria
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12
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Bernini A, Spiga O, Consonni R, Arosio I, Fusi P, Cirri S, Guagliardi A, Niccolai N. Hydration studies on the archaeal protein Sso7d using NMR measurements and MD simulations. BMC STRUCTURAL BIOLOGY 2011; 11:44. [PMID: 22017970 PMCID: PMC3207888 DOI: 10.1186/1472-6807-11-44] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 10/21/2011] [Indexed: 11/25/2022]
Abstract
Background How proteins approach surrounding molecules is fundamental to our understanding of the specific interactions that occur at the surface of proteins. The enhanced surface accessibility of small molecules such as organic solvents and paramagnetic probes to protein binding sites has been observed; however, the molecular basis of this finding has not been fully established. Recently, it has been suggested that hydration dynamics play a predominant role in controlling the distribution of hot spots on surface of proteins. Results In the present study, the hydration of the archaeal multifunctional protein Sso7d from Solfolobus solfataricus was investigated using a combination of computational and experimental data derived from molecular dynamics simulations and ePHOGSY NMR spectroscopy. Conclusions We obtained a convergent protein hydration landscape that indicated how the shape and stability of the Sso7d hydration shell could modulate the function of the protein. The DNA binding domain overlaps with the protein region involved in chaperon activity and this domain is hydrated only in a very small central region. This localized hydration seems to favor intermolecular approaches from a large variety of ligands. Conversely, high water density was found in surface regions of the protein where the ATP binding site is located, suggesting that surface water molecules play a role in protecting the protein from unspecific interactions.
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Affiliation(s)
- Andrea Bernini
- Dipartimento di Biotecnologie, Università degli Studi di Siena, via Fiorentina 1, Siena, Italy
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Abstract
Stable nitroxyl radicals are important tools in chemistry, biophysics, biology, and materials science. Their stability and the sensitivity of their EPR spectra to the local environment make them valuable molecular probes. This review seeks to give an overview of the developments in the field of nitroxide spin probes and their various applications, with the main focus on the pH-sensitive imidazoline nitroxide family.
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Affiliation(s)
- Evelyn Zottler
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
| | - Georg Gescheidt
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, 8010 Graz, Austria
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14
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Kitevski-LeBlanc JL, Evanics F, Prosser RS. Approaches for the measurement of solvent exposure in proteins by 19F NMR. JOURNAL OF BIOMOLECULAR NMR 2009; 45:255-264. [PMID: 19655092 DOI: 10.1007/s10858-009-9359-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2009] [Accepted: 07/14/2009] [Indexed: 05/28/2023]
Abstract
Fluorine NMR is a useful tool to probe protein folding, conformation and local topology owing to the sensitivity of the chemical shift to the local electrostatic environment. As an example we make use of (19)F NMR and 3-fluorotyrosine to evaluate the conformation and topology of the tyrosine residues (Tyr-99 and Tyr-138) within the EF-hand motif of the C-terminal domain of calmodulin (CaM) in both the calcium-loaded and calcium-free states. We critically compare approaches to assess topology and solvent exposure via solvent isotope shifts, (19)F spin-lattice relaxation rates, (1)H-(19)F nuclear Overhauser effects, and paramagnetic shifts and relaxation rates from dissolved oxygen. Both the solvent isotope shifts and paramagnetic shifts from dissolved oxygen sensitively reflect solvent exposed surface areas.
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Affiliation(s)
- Julianne L Kitevski-LeBlanc
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd, North Mississauga, ON, L5L 1C6, Canada
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15
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An NMR method for the determination of protein binding interfaces using TEMPOL-induced chemical shift perturbations. Biochim Biophys Acta Gen Subj 2009; 1790:1368-76. [PMID: 19520148 DOI: 10.1016/j.bbagen.2009.06.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2009] [Revised: 05/28/2009] [Accepted: 06/01/2009] [Indexed: 11/20/2022]
Abstract
BACKGROUND The determination of protein-protein interfaces is of crucial importance to understand protein function and to guide the design of compounds. To identify protein-protein interface by NMR spectroscopy, 13C NMR paramagnetic shifts induced by freely diffusing 4-hydroxy-2, 2, 6, 6-tetramethyl-piperidine-1-oxyl (TEMPOL) are promising, because TEMPOL affects distinct 13C NMR chemical shifts of the solvent accessible nuclei belonging to proteins of interest, while 13C nuclei within the interior of the proteins may be distinguished by a lack of such shifts. METHOD We measured the 13C NMR paramagnetic shifts induced by TEMPOL by recording 13C-(13)C TOCSY spectra for ubiquitin in the free state and the complex state with yeast ubiquitin hydrolase1 (YUH1). RESULTS Upon complexation of ubiquitin with YUH1, 13C NMR paramagnetic shifts associated with the protein binding interface were reduced by 0.05 ppm or more. The identified interfacial atoms agreed with the prior X-ray crystallographic data. CONCLUSIONS The TEMPOL-induced 13C chemical shift perturbation is useful to determine precise protein-protein interfaces. GENERAL SIGNIFICANCE The present method is a useful method to determine protein-protein interface by NMR, because it has advantages in easy sample preparations, simple data analyses, and wide applicabilities.
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16
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Zangger K, Respondek M, Göbl C, Hohlweg W, Rasmussen K, Grampp G, Madl T. Positioning of micelle-bound peptides by paramagnetic relaxation enhancements. J Phys Chem B 2009; 113:4400-6. [PMID: 19256533 DOI: 10.1021/jp808501x] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Many peptides, proteins, and drugs interact with biological membranes, and knowing the mode of binding is essential to understanding their biological functions. To obtain the complete orientation and immersion depth of such a compound, the membrane-mimetic system (micelle) is placed in an aqueous buffer containing the soluble and inert paramagnetic contrast agent Gd(DTPA-BMA). Paramagnetic relaxation enhancements (PREs) of a specific nucleus then depend only on its distance from the surface. The positioning of a structurally characterized compound can be obtained by least-squares fitting of experimental PREs to the micelle center position. This liquid-state NMR approach, which does not rely on isotopic labeling or chemical modification, has been applied to determine the location of the presumed transmembrane region 7 of yeast V-ATPase (TM7) and the membrane-bound antimicrobial peptide CM15 in micelles. TM7 binds in a trans-micelle orientation with the N-terminus being slightly closer to the surface than the C-terminus. CM15 is immersed unexpectedly deep into the micelle with the more hydrophilic side of the helix being closer to the surface than the hydrophobic one.
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Affiliation(s)
- Klaus Zangger
- Institute of Chemistry/Organic and Bioorganic Chemistry, University of Graz, Austria.
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17
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Bernini A, Venditti V, Spiga O, Ciutti A, Prischi F, Consonni R, Zetta L, Arosio I, Fusi P, Guagliardi A, Niccolai N. NMR studies on the surface accessibility of the archaeal protein Sso7d by using TEMPOL and Gd(III)(DTPA-BMA) as paramagnetic probes. Biophys Chem 2008; 137:71-5. [DOI: 10.1016/j.bpc.2008.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2008] [Revised: 07/08/2008] [Accepted: 07/08/2008] [Indexed: 11/27/2022]
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18
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Xu X, Reinle W, Hannemann F, Konarev PV, Svergun DI, Bernhardt R, Ubbink M. Dynamics in a Pure Encounter Complex of Two Proteins Studied by Solution Scattering and Paramagnetic NMR Spectroscopy. J Am Chem Soc 2008; 130:6395-403. [DOI: 10.1021/ja7101357] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xingfu Xu
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Wolfgang Reinle
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Frank Hannemann
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Peter V. Konarev
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Dmitri I. Svergun
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Rita Bernhardt
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
| | - Marcellus Ubbink
- Institute of Chemistry, Leiden University, P.O. Box 9502, NL-2300RA Leiden, The Netherlands, Naturwissenschaftlich-Technische Fakultat III, Institut für Biochemie, Universität des Saarlandes, P.O. Box 151150, D-66041, Saarbrucken, Germany, EMBL Hamburg, Notkestrasse 85, D-22603 Hamburg, Germany, and Institute of Crystallography, Russian Academy of Sciences, Leninsky pr. 59, 117333, Moscow, Russia
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19
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Staple DW, Venditti V, Niccolai N, Elson-Schwab L, Tor Y, Butcher SE. Guanidinoneomycin B recognition of an HIV-1 RNA helix. Chembiochem 2008; 9:93-102. [PMID: 18058789 PMCID: PMC2782590 DOI: 10.1002/cbic.200700251] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Indexed: 01/16/2023]
Abstract
Aminoglycoside antibiotics are small-molecule drugs that bind RNA. The affinity and specificity of aminoglycoside binding to RNA can be increased through chemical modification, such as guanidinylation. Here, we report the binding of guanidinoneomycin B (GNB) to an RNA helix from the HIV-1 frameshift site. The binding of GNB increases the melting temperature (T(m)) of the frameshift-site RNA by at least 10 degrees C, to a point at which a melting transition is not even observed in 2 M urea. A structure of the complex was obtained by using multidimensional heteronuclear NMR spectroscopic methods. We also used a novel paramagnetic-probe assay to identify the site of GNB binding to the surface of the RNA. GNB makes major-groove contacts to two sets of Watson-Crick bases and is in van der Waals contact with a highly structured ACAA tetraloop. Rings I and II of GNB fit into the major groove and form the binding interface with the RNA, whereas rings III and IV are exposed to the solvent and disordered. The binding of GNB causes a broadening of the major groove across the binding site.
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Affiliation(s)
- David W. Staple
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706 (USA)
| | - Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, 53100 Siena (Italy)
| | - Neri Niccolai
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, 53100 Siena (Italy)
| | - Lev Elson-Schwab
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093 (USA)
| | - Yitzhak Tor
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, CA 92093 (USA)
| | - Samuel E. Butcher
- Department of Biochemistry, University of Wisconsin-Madison, 433 Babcock Drive, Madison, WI 53706 (USA)
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20
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Prosser RS, Evanics F, Kitevski JL, Patel S. The measurement of immersion depth and topology of membrane proteins by solution state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3044-51. [DOI: 10.1016/j.bbamem.2007.09.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 09/19/2007] [Accepted: 09/20/2007] [Indexed: 01/22/2023]
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21
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Venditti V, Niccolai N, Butcher SE. Measuring the dynamic surface accessibility of RNA with the small paramagnetic molecule TEMPOL. Nucleic Acids Res 2007; 36:e20. [PMID: 18056080 PMCID: PMC2275091 DOI: 10.1093/nar/gkm1062] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The surface accessibility of macromolecules plays a key role in modulating molecular recognition events. RNA is a complex and dynamic molecule involved in many aspects of gene expression. However, there are few experimental methods available to measure the accessible surface of RNA. Here, we investigate the accessible surface of RNA using NMR and the small paramagnetic molecule TEMPOL. We investigated two RNAs with known structures, one that is extremely stable and one that is dynamic. For helical regions, the TEMPOL probing data correlate well with the predicted RNA surface, and the method is able to distinguish subtle variations in atom depths, such as the relative accessibility of pyrimidine versus purine aromatic carbon atoms. Dynamic motions are also detected by TEMPOL probing, and the method accurately reports a previously characterized pH-dependent conformational transition involving formation of a protonated C-A pair and base flipping. Some loop regions are observed to exhibit anomalously high accessibility, reflective of motions that are not evident within the ensemble of NMR structures. We conclude that TEMPOL probing can provide valuable insights into the surface accessibility and dynamics of RNA, and can also be used as an independent means of validating RNA structure and dynamics in solution.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via Fiorentina 1, 53100 Siena, Italy
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22
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Bernini A, Spiga O, Venditti V, Prischi F, Bracci L, Tong APL, Wong WT, Niccolai N. NMR studies of lysozyme surface accessibility by using different paramagnetic relaxation probes. J Am Chem Soc 2007; 128:9290-1. [PMID: 16848438 DOI: 10.1021/ja062109y] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Paramagnetic probes, whose approach to proteins can be monitored by nuclear magnetic resonance (NMR) studies, have been found to be of primary relevance for investigating protein surfaces' accessibility. Here, a Gd(III) neutral complex which contains two metal ions, [Gd2(L7)(H2O)2], is suggested as a paramagnetic probe particularly suited for systematic NMR investigation of protein surface accessibility, due to an expected high relaxivity and to the lack of electric charge which could favor specific interactions. Hen egg white lysozyme has been used as a model system to verify the absence of preferential approaches of this paramagnetic probe to specific protein moieties by comparing paramagnetic perturbation profiles of 1H-13C HSQC signals obtained in the presence of TEMPOL and [Gd2(L7)(H2O)2]. From the similarity of the measured paramagnetic perturbation profiles induced by the two different probes, specific interactions of [Gd2(L7)(H2O)2] with the enzyme could be ruled out. The large size of the latter probe is suggested to be responsible for the strong paramagnetic perturbations observed for CalphaH groups which are located in convex surface-exposed regions. The combined use of the two probes reveals fine details of the dynamics controlling their approach toward the protein surface.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, I-53100 Siena, Italy
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23
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Venditti V, Bernini A, De Simone A, Spiga O, Prischi F, Niccolai N. MD and NMR studies of alpha-bungarotoxin surface accessibility. Biochem Biophys Res Commun 2007; 356:114-7. [PMID: 17336923 DOI: 10.1016/j.bbrc.2007.02.094] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2007] [Accepted: 02/20/2007] [Indexed: 11/27/2022]
Abstract
Protein surface accessibility represents a dimension of structural biology which has not been discussed in details so far, in spite of its fundamental role in controlling the molecular recognition process. In the present report the surface accessibility of alpha-bungarotoxin, a small and well characterized protein, has been investigated by analyzing its interaction with solvent and paramagnetic molecules in an integrated way. The presence of strong hydration sites, identified by a combined analysis of MD simulation and NMR results, seems to prevent the access of Gd(III)DTPA-BMA to the protein surface. On the contrary, the limited hydration of the alpha-bungarotoxin active site favors frequent encounters between the paramagnetic probe and the protein in the latter region. All the data obtained here for alpha-bungarotoxin suggest that shape and stability of the solvation shell control its surface accessibility and, hence, intermolecular interactions in a way which could be common to many other proteins.
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Affiliation(s)
- Vincenzo Venditti
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, via A. Fiorentina 1, 53100 Siena, Italy
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24
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Vlasie MD, Comuzzi C, van den Nieuwendijk AMCH, Prudêncio M, Overhand M, Ubbink M. Long-Range-Distance NMR Effects in a Protein Labeled with a Lanthanide–DOTA Chelate. Chemistry 2007; 13:1715-23. [PMID: 17115462 DOI: 10.1002/chem.200600916] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A two-thiol reactive lanthanide-DOTA (1,4,7,10-tetraazacyclododecane-N,N',N'',N'''-tetraacetic acid) chelate, CLaNP-3 (CLaNP=caged lanthanide NMR probe), was synthesized for the rigid attachment to cysteine groups on a protein surface, and used to obtain long-range-distance information from the {15N,1H} HSQC spectra of the protein-lanthanide complex. The DOTA ring exhibits several isomers that are in exchange; however, single resonances were observed for most amide groups in the protein, allowing determination of a single, apparent magnetic-susceptibility tensor. Pseudocontact shifts caused by Yb-containing CLaNP-3 were observed for atoms at 15-35 A from the metal. By using Gd-containing CLaNP-3, relaxation effects were observed, allowing distances up to 30 A from the paramagnetic center to be determined accurately. Similar results were obtained with a Gd-DTPA (diethylene-triaminepentaacetic acid) chelate, CLaNP-1, bound in the same bidentate manner to the protein. This study demonstrates that bidentate attachment of a paramagnetic probe enables determination of long-range distances.
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Affiliation(s)
- Monica D Vlasie
- Leiden Institute of Chemistry, Gorlaeus Laboratories Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands
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25
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Steinberg MZ, Breuker K, Elber R, Gerber RB. The dynamics of water evaporation from partially solvated cytochrome c in the gas phase. Phys Chem Chem Phys 2007; 9:4690-7. [PMID: 17700870 DOI: 10.1039/b705905a] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The study of evaporation of water from biological macromolecules is important for the understanding of electrospray mass spectrometry experiments. In electrospray ionization (ESI), electrically charged nanoscale droplets are formed from solutions of, for example, proteins. Then evaporation of the solvent leads to dry protein ions that can be analyzed in the mass spectrometer. In this work the dynamics of water evaporation from native cytochrome c covered by a monolayer of water is studied by molecular dynamics (MD) simulations at constant energy. A model of the initial conditions of the process is introduced. The temperature of the protein drops by about 100 K during the 400 picoseconds of the simulations. This sharp drop in temperature causes the water evaporation rate to decrease by about an order of magnitude, leaving the protein with 50% to 90% of the original water molecules, depending on the initial temperature of the simulation. The structural changes of the protein upon desolvation were considered through calculations of the radius of gyration and the root mean square (RMS) of the protein. A variation of 0.4 A in the radius of gyration, together with an RMS value of less than 3 A, indicates only minor changes in the overall shape of the protein structure. The water coordination number of the solvation shell is much smaller than that for bulk water. The mobility of water is high at the beginning of the simulations and drops as the simulation progresses and the temperature decreases. Incomplete desolvation of protein ions was also observed in recent experiments.
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Affiliation(s)
- Michal Z Steinberg
- Department of Physical Chemistry and the Fritz Haber Research Center, The Hebrew University, 91904, Jerusalem, Israel
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26
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Evanics F, Kitevski JL, Bezsonova I, Forman-Kay J, Prosser RS. 19F NMR studies of solvent exposure and peptide binding to an SH3 domain. Biochim Biophys Acta Gen Subj 2006; 1770:221-30. [PMID: 17182189 DOI: 10.1016/j.bbagen.2006.10.017] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2006] [Revised: 10/02/2006] [Accepted: 10/23/2006] [Indexed: 11/21/2022]
Abstract
(19)F NMR was used to study topological features of the SH3 domain of Fyn tyrosine kinase for both the free protein and a complex formed with a binding peptide. Metafluorinated tyrosine was biosynthetically incorporated into each of 5 residues of the G48M mutant of the SH3 domain (i.e. residues 8, 10, 49 and 54 in addition to a single residue in the linker region to the C-terminal polyhistidine tag). Distinct (19)F NMR resonances were observed and subsequently assigned after separately introducing single phenylalanine mutations. (19)F NMR chemical shifts were dependent on protein concentration above 0.6 mM, suggestive of dimerization via the binding site in the vicinity of the tyrosine side chains. (19)F NMR spectra of Fyn SH3 were also obtained as a function of concentration of a small peptide (2-hydroxynicotinic-NH)-Arg-Ala-Leu-Pro-Pro-Leu-Pro-diaminopropionic acid -NH(2), known to interact with the canonical polyproline II (PPII) helix binding site of the SH3 domain. Based on the (19)F chemical shifts of Tyr8, Tyr49, and Tyr54, as a function of peptide concentration, an equilibrium dissociation constant of 18 +/- 4 microM was obtained. Analysis of the line widths suggested an average exchange rate, k(ex), associated with the peptide-protein two-site exchange, of 5200 +/- 600 s(-1) at a peptide concentration where 96% of the FynSH3 protein was assumed to be bound. The extent of solvent exposure of the fluorine labels was studied by a combination of solvent isotope shifts and paramagnetic effects from dissolved oxygen. Tyr54, Tyr49, Tyr10, and Tyr8, in addition to the Tyr on the C-terminal tag, appear to be fully exposed to the solvent at the metafluoro position in the absence of binding peptide. Tyr54 and, to some extent, Tyr10 become protected from the solvent in the peptide bound state, consistent with known structural data on SH3-domain peptide complexes. These results show the potential utility of (19)F-metafluorotyrosine to probe protein-protein interactions in conjunction with paramagnetic contrast agents.
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Affiliation(s)
- Ferenc Evanics
- Department of Chemistry, University of Toronto, UTM, 3359 Mississauga Rd. North Mississauga, ON, Canada L5L 1C6
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27
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Bernini A, Spiga O, Ciutti A, Venditti V, Prischi F, Governatori M, Bracci L, Lelli B, Pileri S, Botta M, Barge A, Laschi F, Niccolai N. NMR studies of BPTI aggregation by using paramagnetic relaxation reagents. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:856-62. [PMID: 16627014 DOI: 10.1016/j.bbapap.2006.02.013] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Revised: 02/07/2006] [Accepted: 02/27/2006] [Indexed: 11/17/2022]
Abstract
Paramagnetic probes, whose approach to proteins can be monitored by nuclear magnetic resonance (NMR) studies, have been found of primary relevance for investigating protein surfaces accessibility. Here, paramagnetic probes are also suggested for a systematic investigation on protein aggregation. Bovine pancreatic trypsin inhibitor (BPTI) was used as a model system for aggregation by analyzing its interaction with TEMPOL and Gd(III)DTPA-BMA. Some of the measured paramagnetic relaxation rates of BPTI protons exhibited a reverse dependence on protein concentration, which can be attributed to the formation of transient BPTI aggregates.
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Affiliation(s)
- Andrea Bernini
- Biomolecular Structure Research Center and Dipartimento di Biologia Molecolare, Università di Siena, Via A. Fiorentina, I-53100 Siena, Italy
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28
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Huang H, Melacini G. High-resolution protein hydration NMR experiments: Probing how protein surfaces interact with water and other non-covalent ligands. Anal Chim Acta 2006; 564:1-9. [PMID: 17723356 DOI: 10.1016/j.aca.2005.10.049] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2005] [Revised: 10/13/2005] [Accepted: 10/20/2005] [Indexed: 10/25/2022]
Abstract
High-resolution solution NMR experiments are extremely useful to characterize the location and the dynamics of hydrating water molecules at atomic resolution. However, these methods are severely limited by undesired incoherent transfer pathways such as those arising from exchange-relayed intra-molecular cross-relaxation. Here, we review several complementary exchange network editing methods that can be used in conjunction with other types of NMR hydration experiments such as magnetic relaxation dispersion and 1J(NC') measurements to circumvent these limitations. We also review several recent contributions illustrating how the original solution hydration NMR pulse sequence architecture has inspired new approaches to map other types of non-covalent interactions going well beyond the initial scope of hydration. Specifically, we will show how hydration NMR methods have evolved and have been adapted to binding site mapping, ligand screening, protein-peptide and peptide-lipid interaction profiling.
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Affiliation(s)
- Hao Huang
- Department of Chemistry, McMaster University, 1280 Main Street, W. Hamilton, Ont., Canada L8S 4M1
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29
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De Simone A, Spadaccini R, Temussi PA, Fraternali F. Toward the understanding of MNEI sweetness from hydration map surfaces. Biophys J 2006; 90:3052-61. [PMID: 16461400 PMCID: PMC1432101 DOI: 10.1529/biophysj.105.073171] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The binding mechanism of sweet proteins to their receptor, a G-protein-coupled receptor, is not supported by direct structural information. In principle, the key groups responsible for biological activity (glucophores) can be localized on a small structural unit (sweet finger) or spread on a larger surface area. A recently proposed model, called "wedge model", implies a large surface of interaction with the receptor. To explore this model in greater detail, it is necessary to examine the physicochemical features of the surfaces of sweet proteins, since their interaction with the receptor, with respect to that of small sweeteners, is more dependent on general physicochemical properties of the interface, such as electrostatic potential and hydration. In this study, we performed exhaustive molecular dynamics simulations in explicit water of the sweet protein MNEI and of its structural mutant G-16A, whose sweetness is one order of magnitude lower than that of MNEI. Solvent density and self-diffusion calculated from molecular dynamics simulations suggest a likely area of interaction delimited by four stretches arranged as a tetrahedron whose shape is complementary to that of a cavity on the surface of the receptor, in agreement with the wedge model. The suggested area of interaction is amazingly consistent with known mutagenesis data. In addition, the asymmetric hydration of the only helix in both proteins hints at a specific role for this secondary structure element in orienting the protein during the binding process.
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Affiliation(s)
- Alfonso De Simone
- National Institute for Medical Research, NW7 1AA London, United Kingdom
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30
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Friedman R, Nachliel E, Gutman M. Molecular dynamics of a protein surface: ion-residues interactions. Biophys J 2005; 89:768-81. [PMID: 15894639 PMCID: PMC1366628 DOI: 10.1529/biophysj.105.058917] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2005] [Accepted: 04/28/2005] [Indexed: 11/18/2022] Open
Abstract
Time-resolved measurements indicated that protons could propagate on the surface of a protein or a membrane by a special mechanism that enhanced the shuttle of the proton toward a specific site. It was proposed that a suitable location of residues on the surface contributes to the proton shuttling function. In this study, this notion was further investigated by the use of molecular dynamics simulations, where Na(+) and Cl(-) are the ions under study, thus avoiding the necessity for quantum mechanical calculations. Molecular dynamics simulations were carried out using as a model a few Na(+) and Cl(-) ions enclosed in a fully hydrated simulation box with a small globular protein (the S6 of the bacterial ribosome). Three independent 10-ns-long simulations indicated that the ions and the protein's surface were in equilibrium, with rapid passage of the ions between the protein's surface and the bulk. However, it was noted that close to some domains the ions extended their duration near the surface, thus suggesting that the local electrostatic potential hindered their diffusion to the bulk. During the time frame in which the ions were detained next to the surface, they could rapidly shuttle between various attractor sites located under the electrostatic umbrella. Statistical analysis of the molecular dynamics and electrostatic potential/entropy consideration indicated that the detainment state is an energetic compromise between attractive forces and entropy of dilution. The similarity between the motion of free ions next to a protein and the proton transfer on the protein's surface are discussed.
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Affiliation(s)
- Ran Friedman
- Laser Laboratory for Fast Reactions in Biology, Department of Biochemistry, The George S. Wise Faculty for Life Sciences, Tel Aviv University, Israel
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31
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Varrazzo D, Bernini A, Spiga O, Ciutti A, Chiellini S, Venditti V, Bracci L, Niccolai N. Three-dimensional computation of atom depth in complex molecular structures. Bioinformatics 2005; 21:2856-60. [PMID: 15827080 DOI: 10.1093/bioinformatics/bti444] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION For a complex molecular system the delineation of atom-atom contacts, exposed surface and binding sites represents a fundamental step to predict its interaction with solvent, ligands and other molecules. Recently, atom depth has been also considered as an additional structural descriptor to correlate protein structure with folding and functional properties. The distance between an atom and the nearest water molecule or the closest surface dot has been proposed as a measure of the atom depth, but, in both cases, the 3D character of depth is largely lost. In the present study, a new approach is proposed to calculate atom depths in a way that the molecular shape can be taken into account. RESULTS An algorithm has been developed to calculate intersections between the molecular volume and spheres centered on the atoms whose depth has to be quantified. Many proteins with different size and shape have been chosen to compare the results obtained from distance-based and volume-based depth calculations. From the wealth of experimental data available for hen egg white lysozyme, H/D exchange rates and TEMPOL induced paramagnetic perturbations have been analyzed both in terms of depth indexes and of atom distances to the solvent accessible surface. The algorithm here proposed yields better correlations between experimental data and atom depth, particularly for those atoms which are located near to the protein surface. AVAILABILITY Instructions to obtain source code and the executable program are available either from http://sienabiografix.com or http://sadic.sourceforge.net CONTACT niccolai@unisi.it SUPPLEMENTARY INFORMATION http://www.Sienabiogzefix.com/publication.
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Affiliation(s)
- Daniele Varrazzo
- Biomolecular Structure Research Center and Department of Molecular Biology, Università di Siena, I-53100 Siena, Italy
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32
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Sakakura M, Noba S, Luchette PA, Shimada I, Prosser RS. An NMR Method for the Determination of Protein-Binding Interfaces Using Dioxygen-Induced Spin−Lattice Relaxation Enhancement. J Am Chem Soc 2005; 127:5826-32. [PMID: 15839680 DOI: 10.1021/ja047825j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Using oxygen as a paramagnetic probe, researchers can routinely study topologies and protein-binding interfaces by NMR. The paramagnetic contribution to the amide (1)H spin-lattice relaxation rates (R(1)(P)) have been studied for uniformly (2)H,(15)N-labeled FB protein, a 60-residue three-helix bundle, constituting the B domain of protein A. Through TROSY versions of inversion-recovery experiments, R(1)(P) could be determined. R(1)(P) was then measured in the presence of a stoichiometric equivalent of an unlabeled Fc fragment of immunoglobulin (Ig) G, and the ratio of R(1)(P) of the FB-Fc complex to that of free FB [i.e., R(1)(P)(complex)/R(1)(P)(free)] was determined for each observable residue. Regions of helix I and helix II, which were previously known to interact with Fc, were readily identified as belonging to the binding interface by their characteristically reduced values of R(1)(P)(complex)/R(1)(P)(free). The method of comparing oxygen-induced spin-lattice relaxation rates of free protein and protein-protein complexes, to detect binding interfaces, offers greater sensitivity than chemical shift perturbation, while it is not necessary to heavily deuterate the labeled protein, as is the case in cross saturation experiments.
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Affiliation(s)
- M Sakakura
- Contribution from the Graduate School of Pharmaceutical Sciences, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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Bernini A, Spiga O, Ciutti A, Chiellini S, Menciassi N, Venditti V, Niccolai N. On the dynamics of water molecules at the protein solute interfaces. HOMEOPATHY 2004; 93:199-202. [PMID: 15532699 DOI: 10.1016/j.homp.2004.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Proteins, with the large variety of chemical groups they present at their molecular surface, are a class of molecules which can be very informative on most of the possible solute-solvent interactions. Hen egg white lysozyme has been used as a probe to investigate the complex solvent dynamics occurring at the protein surface, by analysing the results obtained from Nuclear Magnetic Resonance, X-ray diffractometry and Molecular Dynamics simulations. A consistent overall picture for the dynamics of water molecules close to the protein is obtained, suggesting that a rapid exchange occurs, in a picosecond timescale, among all the possible hydration surface sites both in solution and the solid state, excluding the possibility that solvent molecules can form liquid-crystal-like supramolecular adducts, which have been proposed as a molecular basis of 'memory of water'.
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Affiliation(s)
- A Bernini
- Department of Molecular Biology, Biomolecular Structure Research Center, University of Siena, Via Fiorentina 1, 53100 Siena, Italy
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Anick DJ. High sensitivity 1H-NMR spectroscopy of homeopathic remedies made in water. Altern Ther Health Med 2004; 4:15. [PMID: 15518588 PMCID: PMC534805 DOI: 10.1186/1472-6882-4-15] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2004] [Accepted: 11/01/2004] [Indexed: 11/12/2022]
Abstract
Background The efficacy of homeopathy is controversial. Homeopathic remedies are made via iterated shaking and dilution, in ethanol or in water, from a starting substance. Remedies of potency 12 C or higher are ultra-dilute (UD), i.e. contain zero molecules of the starting material. Various hypotheses have been advanced to explain how a UD remedy might be different from unprepared solvent. One such hypothesis posits that a remedy contains stable clusters, i.e. localized regions where one or more hydrogen bonds remain fixed on a long time scale. High sensitivity proton nuclear magnetic resonance spectroscopy has not previously been used to look for evidence of differences between UD remedies and controls. Methods Homeopathic remedies made in water were studied via high sensitivity proton nuclear magnetic resonance spectroscopy. A total of 57 remedy samples representing six starting materials and spanning a variety of potencies from 6 C to 10 M were tested along with 46 controls. Results By presaturating on the water peak, signals could be reliably detected that represented H-containing species at concentrations as low as 5 μM. There were 35 positions where a discrete signal was seen in one or more of the 103 spectra, which should theoretically have been absent from the spectrum of pure water. Of these 35, fifteen were identified as machine-generated artifacts, eight were identified as trace levels of organic contaminants, and twelve were unexplained. Of the unexplained signals, six were seen in just one spectrum each. None of the artifacts or unexplained signals occurred more frequently in remedies than in controls, using a p < .05 cutoff. Some commercially prepared samples were found to contain traces of one or more of these small organic molecules: ethanol, acetate, formate, methanol, and acetone. Conclusion No discrete signals suggesting a difference between remedies and controls were seen, via high sensitivity 1H-NMR spectroscopy. The results failed to support a hypothesis that remedies made in water contain long-lived non-dynamic alterations of the H-bonding pattern of the solvent.
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Affiliation(s)
- David J Anick
- Harvard Medical School Mailman Building 123, McLean Hospital, Belmont, MA 02478, USA.
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Chang CC, Yeh XC, Lee HT, Lin PY, Kan LS. Refolding of lysozyme by quasistatic and direct dilution reaction paths: a first-order-like state transition. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:011904. [PMID: 15324085 DOI: 10.1103/physreve.70.011904] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2003] [Indexed: 05/24/2023]
Abstract
A first-order-like state transition model is considered to be a global reaction mechanism to directly folded proteins from an unfolded state to its native form. In order to verify the general applicability of this mechanism, we used lysozyme as a model protein. It was fully unfolded by 4.5 M urea, 0.1 M dithiothreitol (DTT) in pH 3 and refolded to its native form by way of an overcritical reaction path (a quasistatic process) or directly crossing transition boundary path (a directly dilution process). In addition to the two states coexisting in the direct folding path, lysozyme might be trapped in a glassy state. However, it can escape from the glassy state by concentration twice. This indicates the existence of a state transition line or boundary in the direct folding reaction. However, lysozyme can continuously fold from unfolded to native by an overcritical reaction path. During the overcritical path, four stable folding intermediates and native lysozyme were obtained. The secondary structures, particle size distributions, thermal stabilities, and oxidation state of disulfide bonds of folding intermediates were analyzed by circular dichroism spectra, dynamic light scattering, differential scanning calorimetry, and Raman spectra, respectively. According to the data, the intermediates of both the overcritical reaction and the direct crossing transition boundary paths can be described by a common concept pertaining to a model that undergoes collapse, sequential, and first-order-like state transition. This indicated that protein folding by way of different reaction paths might follow a similar folding mechanism-i.e., a mechanism of overcritical folding of intermediates. A protein folding reaction diagram is postulated and discussed. In spite of a global interaction mechanism the alpha -helix is formed prior to the beta -sheet, which may indicate that protein folding is initiated by local interactions.
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Affiliation(s)
- Chia-Ching Chang
- Department of Physics, National Dong Hwa University, Hualien, Taiwan 97401.
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