1
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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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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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3
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Current Progress in Understanding the Structure and Function of Sweet Taste Receptor. J Mol Neurosci 2020; 71:234-244. [PMID: 32607758 DOI: 10.1007/s12031-020-01642-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 06/19/2020] [Indexed: 10/24/2022]
Abstract
The sweet taste receptor, which was identified approximately 20 years ago, mediates sweet taste recognition in humans and other vertebrates. With the development of genomics, metabonomics, structural biology, evolutionary biology, physiology, and neuroscience, as well as technical advances in these areas, our understanding of this important protein has resulted in substantial progress. This article reviews the structure, function, genetics, and evolution of the sweet taste receptor and offers meaningful insights into this G protein-coupled receptor, which may be helpful guidances for personalized feeding, diet, and medicine. Prospective directions for research on sweet taste receptors have also been proposed.
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4
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Biswas AD, Barone V, Amadei A, Daidone I. Length-scale dependence of protein hydration-shell density. Phys Chem Chem Phys 2020; 22:7340-7347. [PMID: 32211621 DOI: 10.1039/c9cp06214a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Here we present a computational approach based on molecular dynamics (MD) simulation to study the dependence of the protein hydration-shell density on the size of the protein molecule. The hydration-shell density of eighteen different proteins, differing in size, shape and function (eight of them are antifreeze proteins), is calculated. The results obtained show that an increase in the hydration-shell density, relative to that of the bulk, is observed (in the range of 4-14%) for all studied proteins and that this increment strongly correlates with the protein size. In particular, a decrease in the density increment is observed for decreasing protein size. A simple model is proposed in which the basic idea is to approximate the protein molecule as an effective ellipsoid and to partition the relevant parameters, i.e. the solvent-accessible volume and the corresponding solvent density, into two regions: inside and outside the effective protein ellipsoid. It is found that, within the model developed here, almost all of the hydration-density increase is located inside the protein ellipsoid, basically corresponding to pockets within, or at the surface of the protein molecule. The observed decrease in the density increment is caused by the protein size only and no difference is found between antifreeze and non-antifreeze proteins.
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Affiliation(s)
- Akash Deep Biswas
- Department of Physical and Chemical Sciences, University of L'Aquila, via Vetoio (Coppito 1), 67010 L'Aquila, Italy.
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5
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Donnarumma F, Leone S, Delfi M, Emendato A, Ami D, Laurents DV, Natalello A, Spadaccini R, Picone D. Probing structural changes during amyloid aggregation of the sweet protein MNEI. FEBS J 2019; 287:2808-2822. [DOI: 10.1111/febs.15168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 11/20/2019] [Accepted: 12/05/2019] [Indexed: 12/13/2022]
Affiliation(s)
- Federica Donnarumma
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Serena Leone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Masoud Delfi
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Alessandro Emendato
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
| | - Diletta Ami
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Douglas V. Laurents
- Institute of Physical Chemistry ‘Rocasolano’ Consejo Superior de Investigaciones Científicas Madrid Spain
| | - Antonino Natalello
- Department of Biotechnology and Biosciences University of Milano‐Bicocca Italy
| | - Roberta Spadaccini
- Department of Science and Technology Università degli Studi del Sannio Benevento Italy
| | - Delia Picone
- Department of Chemical Sciences University of Naples ‘Federico II’ Napoli Italy
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6
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The Flexible Loop is a New Sweetness Determinant Site of the Sweet-Tasting Protein: Characterization of Novel Sweeter Mutants of the Single-Chain Monellin (MNEI). Chem Senses 2019; 44:607-614. [DOI: 10.1093/chemse/bjz057] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
AbstractThe single-chain monellin (MNEI) displays same sweet potency as the natural monellin protein. To identify critical residues determining its sweetness, residues located at the loops region were selected for mutagenesis analysis. Mutations of positive-charge residues R31, R53, and R82 consistently led to obvious decrease of sweetness, whereas mutations of negative-charge residues resulted in variable sweet potency. Of note, the E50N mutant in the loop region linking the 2 natural chains showed significantly increased sweetness. Mutations of this residue to M or K led to similar effects, in accordance with the so-called wedge model for explanation of the sweet protein–receptor interaction. Homology modeling was carried out with the firstly reported crystal structure of sweet taste receptor (from medaka fish) as the template, and molecular docking and dynamics simulations suggested that flexible conformations of specific residues located in the loops region play essential roles for the interaction with the receptor and the sweetness of the protein. Moreover, obvious additive effects were found for the sweetness as 2 double-site mutants (E50N/Y65R and E2N/E50N) displayed increased sweetness than their single-site mutants. Our results revealed the flexible loop L23 linking the 2 natural chains as a novel sweetness determinant site of the sweet protein monellin and raised a series of new sweeter mutants, which could provide helpful guidance for molecular designing the sweet-tasting proteins.
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7
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Sheu SY, Liu YC, Zhou JK, Schlag EW, Yang DY. Surface Topography Effects of Globular Biomolecules on Hydration Water. J Phys Chem B 2019; 123:6917-6932. [PMID: 31282162 DOI: 10.1021/acs.jpcb.9b03734] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Hydration water serves as a microscopic manifestation of structural stability and functions of biomolecules. To develop bio-nanomaterials in applications, it is important to study how the surface topography and heterogeneity of biomolecules result in their diversity of the hydration dynamics and energetics. We here performed molecular dynamics simulations combined with the steered molecular dynamics and umbrella sampling to investigate the dynamics and escape process associated with the free energy change of water molecules close to a globular biomolecule, i.e., hemoglobin (Hb) and G-quadruplex DNA (GDNA). The residence time, power of long-time tail, and dipole relaxation time were found to display drastic changes within the averaged hydration shell of 3.0-5.0 Å. Compared with bulk water, in the inner hydration shell, the water dipole moment displays a slower relaxation process and is more oriented toward GDNA than toward Hb, forming a hedgehog-like structure when it surrounds GDNA. In particular, a spine water structure is observed in the GDNA narrow groove. The water isotope effect not only prolongs the dynamic time scales of libration motion in the inner hydration shell and the dipole relaxation processes in the bulk but also strengthens the DNA spine water structure. The potential of the mean force profile reflects the integrity of the hydration shell structure and enables us to obtain detailed insights into the structures formed by water, such as the caged H-bond network and the edge bridge structures; it also reveals that local hydration shell free energy (LHSFE) depends on H-bond rupture processes and ranges from 0.2 to 4.2 kcal/mol. Our results demonstrate that the surface topography of a biomolecule influences the integrity of the hydration shell structure and LHSFE. Our studies are able to identify various further applications in the areas of microfluid devices and nano-dewetting on bioinspired surfaces.
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Affiliation(s)
- Sheh-Yi Sheu
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan.,Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Yu-Cheng Liu
- Institute of Biomedical Informatics , National Yang-Ming University , Taipei 112 , Taiwan
| | - Jia-Kai Zhou
- Department of Life Sciences and Institute of Genome Sciences , National Yang-Ming University , Taipei 112 , Taiwan
| | - Edward W Schlag
- Institut für Physikalische und Theoretische Chemie , TU-München , Lichtenbergstr. 4 , 85748 Garching , Germany
| | - Dah-Yen Yang
- Institute of Atomic and Molecular Sciences , Academia Sinica , Taipei 106 , Taiwan
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8
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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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9
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Simonelli L, Pedotti M, Bardelli M, Jurt S, Zerbe O, Varani L. Mapping Antibody Epitopes by Solution NMR Spectroscopy: Practical Considerations. Methods Mol Biol 2018; 1785:29-51. [PMID: 29714010 DOI: 10.1007/978-1-4939-7841-0_3] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Identifying an epitope, the region of the antigen in contact with an antibody, is useful in both basic and pharmaceutical research, as well as in vaccine design. Solution NMR spectroscopy is particularly well suited to the residue level characterization of intermolecular interfaces, including antibody-antigen interactions, and thus to epitope identification. Here, we describe the use of NMR for residue level characterization of protein epitopes, focusing on experimental protocols and practical considerations, highlighting advantages and drawbacks of the approach.
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Affiliation(s)
- Luca Simonelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Mattia Pedotti
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Marco Bardelli
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland
| | - Simon Jurt
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Oliver Zerbe
- Department of Chemistry, University of Zurich, Zurich, Switzerland
| | - Luca Varani
- Institute for Research in Biomedicine, Universita' della Svizzera italiana (USI), Bellinzona, Switzerland.
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10
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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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11
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Spadaccini R, Leone S, Rega MF, Richter C, Picone D. Influence of pH on the structure and stability of the sweet protein MNEI. FEBS Lett 2016; 590:3681-3689. [DOI: 10.1002/1873-3468.12437] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 11/11/2022]
Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Scienze e Tecnologie; Università del Sannio; Benevento Italy
| | - Serena Leone
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II; Naples Italy
| | | | | | - Delia Picone
- Dipartimento di Scienze Chimiche; Università di Napoli Federico II; Naples Italy
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12
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Leone S, Picone D. Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein. PLoS One 2016; 11:e0158372. [PMID: 27340829 PMCID: PMC4920389 DOI: 10.1371/journal.pone.0158372] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/14/2016] [Indexed: 11/18/2022] Open
Abstract
MNEI is a single chain derivative of monellin, a plant protein that can interact with the human sweet taste receptor, being therefore perceived as sweet. This unusual physiological activity makes MNEI a potential template for the design of new sugar replacers for the food and beverage industry. Unfortunately, applications of MNEI have been so far limited by its intrinsic sensitivity to some pH and temperature conditions, which could occur in industrial processes. Changes in physical parameters can, in fact, lead to irreversible protein denaturation, as well as aggregation and precipitation. It has been previously shown that the correlation between pH and stability in MNEI derives from the presence of a single glutamic residue in a hydrophobic pocket of the protein. We have used molecular dynamics to study the consequences, at the atomic level, of the protonation state of such residue and have identified the network of intramolecular interactions responsible for MNEI stability at acidic pH. Based on this information, we have designed a pH-independent, stabilized mutant of MNEI and confirmed its increased stability by both molecular modeling and experimental techniques.
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Affiliation(s)
- Serena Leone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Delia Picone
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
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13
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Lee JW, Cha JE, Jo HJ, Kong KH. Multiple mutations of the critical amino acid residues for the sweetness of the sweet-tasting protein, brazzein. Food Chem 2013; 138:1370-3. [DOI: 10.1016/j.foodchem.2012.10.140] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2012] [Revised: 10/09/2012] [Accepted: 10/25/2012] [Indexed: 11/30/2022]
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14
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Kaas Q, Craik DJ. NMR of plant proteins. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2013; 71:1-34. [PMID: 23611313 DOI: 10.1016/j.pnmrs.2013.01.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Accepted: 01/21/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Quentin Kaas
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, Queensland 4072, Australia
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15
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Amino acid sensing in the gastrointestinal tract. Amino Acids 2012; 45:451-61. [DOI: 10.1007/s00726-012-1371-2] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 07/14/2012] [Indexed: 12/24/2022]
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16
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Pagano K, Torella R, Foglieni C, Bugatti A, Tomaselli S, Zetta L, Presta M, Rusnati M, Taraboletti G, Colombo G, Ragona L. Direct and allosteric inhibition of the FGF2/HSPGs/FGFR1 ternary complex formation by an antiangiogenic, thrombospondin-1-mimic small molecule. PLoS One 2012; 7:e36990. [PMID: 22606323 PMCID: PMC3351436 DOI: 10.1371/journal.pone.0036990] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 04/11/2012] [Indexed: 11/18/2022] Open
Abstract
Fibroblast growth factors (FGFs) are recognized targets for the development of therapies against angiogenesis-driven diseases, including cancer. The formation of a ternary complex with the transmembrane tyrosine kinase receptors (FGFRs), and heparan sulphate proteoglycans (HSPGs) is required for FGF2 pro-angiogenic activity. Here by using a combination of techniques including Nuclear Magnetic Resonance, Molecular Dynamics, Surface Plasmon Resonance and cell-based binding assays we clarify the molecular mechanism of inhibition of an angiostatic small molecule, sm27, mimicking the endogenous inhibitor of angiogenesis, thrombospondin-1. NMR and MD data demonstrate that sm27 engages the heparin-binding site of FGF2 and induces long-range dynamics perturbations along FGF2/FGFR1 interface regions. The functional consequence of the inhibitor binding is an impaired FGF2 interaction with both its receptors, as demonstrated by SPR and cell-based binding assays. We propose that sm27 antiangiogenic activity is based on a twofold-direct and allosteric-mechanism, inhibiting FGF2 binding to both its receptors.
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Affiliation(s)
- Katiuscia Pagano
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Rubben Torella
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Chiara Foglieni
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Bergamo, Italy
| | - Antonella Bugatti
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Simona Tomaselli
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Lucia Zetta
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
| | - Marco Presta
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Marco Rusnati
- Department of Biomedical Sciences and Biotechnology, School of Medicine, University of Brescia, Brescia, Italy
| | - Giulia Taraboletti
- Department of Oncology, Mario Negri Institute for Pharmacological Research, Bergamo, Italy
| | - Giorgio Colombo
- Istituto di Chimica del Riconoscimento Molecolare, Consiglio Nazionale delle Ricerche, Milano, Italy
- * E-mail: (LR); (GC)
| | - Laura Ragona
- Laboratorio NMR, Istituto per lo Studio delle Macromolecole, Consiglio Nazionale delle Ricerche, Milano, Italy
- * E-mail: (LR); (GC)
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17
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Yoon SY, Kong JN, Jo DH, Kong KH. Residue mutations in the sweetness loops for the sweet-tasting protein brazzein. Food Chem 2011. [DOI: 10.1016/j.foodchem.2011.06.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Temussi PA. Determinants of sweetness in proteins: a topological approach. J Mol Recognit 2011; 24:1033-42. [DOI: 10.1002/jmr.1152] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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19
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Gnanavel M, Serva Peddha M. Identification of novel sweet protein for nutritional applications. Bioinformation 2011; 7:112-4. [PMID: 22125379 PMCID: PMC3218311 DOI: 10.6026/97320630007112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2011] [Accepted: 05/30/2011] [Indexed: 11/23/2022] Open
Abstract
The prevalence of obesity and diabetes has increased exponentially in recent years around the globe, especially in India. Sweet proteins have the potential to substitute the sugars, by acting as natural, good and low calorie sweeteners. They also do not trigger a demand for insulin in diabetic patients unlike sucrose. In humans, the sweet taste perception is mainly due to taste-specific G protein-coupled heterodimeric receptors T1R2-T1R3. These receptors recognize diverse natural and synthetic sweeteners such as monelin, brazzein, thaumatin, curculin, mabinlin, miraculin and pentadin. Structural modeling of new sweetener proteins will be a great leap in further advancement of knowledge and their utility as sweeteners. We have explored the fingerprints of sweetness by studying the aminoacid composition and structure properties of the above proteins. The structural analysis of monellin revealed that the individual A or B chains of monellin are not contributing to its sweetness. However, the native conformation and ionic interaction between AspB7 of monellin with active site of T1R2-T1R3 receptor, along with hydrogen bonding stability of IleB6 and IleB8 are responsible for the sweet taste. Based on structural similarity search, we found a new hypothetical protein from Shewanella loihica, which has the presence of Asp(32) with adjacent isoleucine residues. Further, we examined the lead protein by two-step docking for the study of interaction of functionally conserved residues with receptors. The identified protein showed similar ionic and hydrophobic interactions with monelin. This gives a promising opportunity to explore this protein for potential health application in the low calorie sweetener industry viz., soft drinks, snacks, food, chocolate industries etc.
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Affiliation(s)
- Mutharasu Gnanavel
- Biochemistry and Nutrition, Central Food Technological Research Institute, Mysore, India – 570 020
| | - Muthukumar Serva Peddha
- Biochemistry and Nutrition, Central Food Technological Research Institute, Mysore, India – 570 020
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Templeton CM, Ostovar pour S, Hobbs JR, Blanch EW, Munger SD, Conn GL. Reduced sweetness of a monellin (MNEI) mutant results from increased protein flexibility and disruption of a distant poly-(L-proline) II helix. Chem Senses 2011; 36:425-34. [PMID: 21343241 DOI: 10.1093/chemse/bjr007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monellin is a highly potent sweet-tasting protein but relatively little is known about how it interacts with the sweet taste receptor. We determined X-ray crystal structures of 3 single-chain monellin (MNEI) proteins with alterations at 2 core residues (G16A, V37A, and G16A/V37A) that induce 2- to 10-fold reductions in sweetness relative to the wild-type protein. Surprisingly, no changes were observed in the global protein fold or the positions of surface amino acids important for MNEI sweetness that could explain these differences in protein activity. Differential scanning calorimetry showed that while the thermal stability of each mutant MNEI was reduced, the least sweet mutant, G16A-MNEI, was not the least stable protein. In contrast, solution spectroscopic measurements revealed that changes in protein flexibility and the C-terminal structure correlate directly with protein activity. G16A mutation-induced disorder in the protein core is propagated via changes to hydrophobic interactions that disrupt the formation and/or position of a critical C-terminal poly-(L-proline) II helix. These findings suggest that MNEI interaction with the sweet taste receptor is highly sensitive to the relative positions of key residues across its protein surface and that loss of sweetness in G16A-MNEI may result from an increased entropic cost of binding.
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Affiliation(s)
- Catherine M Templeton
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA
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New insights into the characteristics of sweet and bitter taste receptors. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2011; 291:191-226. [PMID: 22017977 DOI: 10.1016/b978-0-12-386035-4.00006-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Understanding the molecular bases of taste is of primary importance for the field of human senses as well as for translational medical science. This chapter describes the complexity of the mechanism of action of sweet, bitter, and umami receptors. Most molecular weight sweeteners interact with orthosteric sites of the sweet receptor. The mechanism of action of sweet proteins is more difficult to interpret. In the only general mechanism proposed for the action of sweet proteins, the "wedge model," it is hypothesized that proteins bind to an external active site of the active conformation of the sweet receptor. This model can be updated by building topologically correct complexes of proteins with the receptor. Among the recent advances that will be described here are the discovery of taste modulators and the possibility that certain bitter compounds are recognized by the umami receptor.
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Linser R, Fink U, Reif B. Probing Surface Accessibility of Proteins Using Paramagnetic Relaxation in Solid-State NMR Spectroscopy. J Am Chem Soc 2009; 131:13703-8. [DOI: 10.1021/ja903892j] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rasmus Linser
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Uwe Fink
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
| | - Bernd Reif
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Rössle-Str. 10, D-13125 Berlin, Germany and Charité Universitätsmedizin, D-10115 Berlin, Germany
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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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Bhowmik A, Ellena JF, Bryant RG, Cafiso DS. Spin-diffusion couples proton relaxation rates for proteins in exchange with a membrane interface. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2008; 194:283-288. [PMID: 18723378 PMCID: PMC2581927 DOI: 10.1016/j.jmr.2008.07.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Revised: 07/17/2008] [Accepted: 07/18/2008] [Indexed: 05/26/2023]
Abstract
Changes in nuclear spin-lattice relaxation rates that are induced by a freely diffusing paramagnetic relaxation agent are examined for a protein in solution and compared to the case where the protein binds to a membrane. In the solution case, the intramolecular cross-relaxation rates are modest and large differences are observed in the oxygen induced protein-proton relaxation rates. In the case where a dynamic equilibrium between solution and membrane-bound environments is established, the intramolecular (1)H cross-relaxation rates for the protein protons increase dramatically because of the slow reorientational motion in the membrane-bound environment. As a consequence, all protein protons relax with nearly the same spin-lattice relaxation rate constants when bound to the membrane, and site specific relaxation effects of the diffusing paramagnet are suppressed. Slowly reorienting sites or rotationally immobilized sites sampled by observable molecules in vivo will demonstrate similar relaxation leveling effects.
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Affiliation(s)
| | | | - Robert G. Bryant
- Authors to whom correspondence should be addressed. FAX: 434-924-3567. E-mail addresses: (DSC); (RGB)
| | - David S. Cafiso
- Authors to whom correspondence should be addressed. FAX: 434-924-3567. E-mail addresses: (DSC); (RGB)
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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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26
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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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Teng CL, Hinderliter B, Bryant RG. Oxygen accessibility to ribonuclease a: quantitative interpretation of nuclear spin relaxation induced by a freely diffusing paramagnet. J Phys Chem A 2007; 110:580-8. [PMID: 16405330 DOI: 10.1021/jp0526593] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The nuclear spin relaxation induced by a freely diffusing paramagnetic center provides a direct measure of intermolecular accessibility. A number of factors are involved in a quantitative interpretation of relaxation data including excluded volume effects, solvation differences, and the details of the electron spin relaxation in the paramagnetic center. In the case where the electron relaxation time is short compared with correlation times describing the electron-nuclear coupling, the nuclear spin relaxation rates may be related to the effective local concentration of the paramagnetic center at different locations about the solute of interest. The local concentrations may in turn be related to differences in the local free energies of interaction between the diffusing paramagnet and the cosolute. We demonstrate this approach for the case of ribonuclease A and deduce surface free energy differences for a large number of protein proton sites. We find that the oxygen accessibility is poorly represented by hard-sphere models such as computed solvent or steric accessibility. There is a distribution of local intermolecular interactions with a width of the order of RT that dominates the report of the intermolecular exploration of the protein by this simple solute.
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Affiliation(s)
- Ching-Ling Teng
- The Biophysics Program and Chemistry Department, University of Virginia, Charlottesville, Virginia 22904-4319, USA
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28
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Fumino K, Diakova G, Andersen JD, Brown ML, Bryant RG. Solvation and Intermolecular Exploration of Drug Molecule Fragments. J SOLUTION CHEM 2007. [DOI: 10.1007/s10953-007-9142-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Hobbs JR, Munger SD, Conn GL. Monellin (MNEI) at 1.15 A resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 2007; 63:162-7. [PMID: 17329805 PMCID: PMC2330190 DOI: 10.1107/s1744309107005271] [Citation(s) in RCA: 26] [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: 12/20/2006] [Accepted: 01/31/2007] [Indexed: 11/11/2022]
Abstract
The X-ray crystal structure of a single-chain monellin protein (MNEI) has been determined at 1.15 A resolution. The model was refined to convergence employing anisotropic displacement parameters and riding H atoms to produce a final model with R(work) and R(free) values of 0.132 and 0.162, respectively. The crystal contains a single MNEI protein in the asymmetric unit and unusually lacks the dimer interface observed in all previous crystal structures of monellin and its single-chain derivatives. The high resolution allowed a more detailed view of MNEI than previously possible, with 38 of the 96 residues modelled with alternative side-chain conformations, including four core residues Thr12, Cys41, Leu62 and Ile75. Four stably bound negative ions were also located, providing new insight into potential electrostatic interactions of MNEI with the largely negatively charged surface of the sweet taste receptor T1R2-T1R3.
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Affiliation(s)
- J. R. Hobbs
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M60 1QD, England
| | - S. D. Munger
- Department of Anatomy and Neurobiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - G. L. Conn
- Manchester Interdisciplinary Biocentre, Faculty of Life Sciences, University of Manchester, Manchester M60 1QD, England
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30
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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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Temussi P. The sweet taste receptor: a single receptor with multiple sites and modes of interaction. ADVANCES IN FOOD AND NUTRITION RESEARCH 2007; 53:199-239. [PMID: 17900500 DOI: 10.1016/s1043-4526(07)53006-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Elucidation of the molecular bases of sweet taste is very important not only for its intrinsic biological significance but also for the design of new artificial sweeteners. Up to few years ago design was complicated by the common belief that different classes of sweet compounds, notably sweet proteins, might interact with different receptors altogether. The recent identification and functional expression of the receptor for sweet taste have shown that there is but one receptor, drastically changing our approach to the development of new sweeteners. The explanation of how the sweet receptor can bind several different classes of molecules is that rather than multiple receptors there are, apparently, multiple sites on the single sweet taste receptor. In this chapter, the mechanisms of interaction of small and macromolecular sweet molecules will be examined, with particular emphasis on sweet proteins. Systematic homology modeling yields reliable models of all possible heterodimers of the human T1R2 and T1R3 sequences with the closed (A) and open (B) conformations of one of the metabotropic glutamate receptors (mGluR1), used as template. The most important result of these studies is the "wedge model," the first explanation of the taste of sweet proteins. In addition, it was shown that simultaneous binding to the A and B sites is not possible with two large sweeteners but is possible with a small molecule in site A and a large one in site B. This observation accounted for the first time for the peculiar phenomenon of synergy between some sweeteners.
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Affiliation(s)
- Pierandrea Temussi
- Dipartimento di Chimica, Università di Napoli Federico II, Via Cinthia, Napoli I-80126, Italy
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Esposito V, Gallucci R, Picone D, Saviano G, Tancredi T, Temussi PA. The Importance of Electrostatic Potential in The Interaction of Sweet Proteins with the Sweet Taste Receptor. J Mol Biol 2006; 360:448-56. [PMID: 16764888 DOI: 10.1016/j.jmb.2006.05.020] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2006] [Revised: 05/05/2006] [Accepted: 05/09/2006] [Indexed: 11/19/2022]
Abstract
In addition to many small molecular mass sweeteners there are in nature a few sweet proteins. The molecular volume of sweet proteins is so different from that of common sweeteners that it was difficult to understand how molecules as large as proteins can activate a receptor designed to host small molecules. We have recently shown that sweet proteins can activate the sweet receptor by a mechanism of interaction, called ''wedge model", in which proteins fit a large cavity of the receptor with wedge-shaped surfaces of their structures. In order to substantiate this model we have designed, expressed and characterized seven mutants of MNEI, a single chain monellin. Three uncharged residues of the interaction surface, Met42, Tyr63 and Tyr65, were changed either into acidic or basic residues whereas Asp68, a key acidic residue, was changed into a basic one. As a general trend, we observe that an increase of the negative charge is much more detrimental for sweetness than an increase of positive charge. In addition we show that by a careful choice of a residue at the center of the interface between MNEI and receptor, it is possible even to increase the sweetness of MNEI. These results are fully consistent with the wedge model.
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Affiliation(s)
- Veronica Esposito
- Department of Chemistry, Università di Napoli Federico II, IT-80126 Naples, Italy
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33
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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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Teng CL, Bryant RG. Spin relaxation measurements of electrostatic bias in intermolecular exploration. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2006; 179:199-205. [PMID: 16386442 DOI: 10.1016/j.jmr.2005.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Revised: 12/09/2005] [Accepted: 12/09/2005] [Indexed: 05/05/2023]
Abstract
We utilize the paramagnetic contribution to proton spin-lattice relaxation rate constants induced by freely diffusing charged paramagnetic centers to investigate the effect of charge on the intermolecular exploration of a protein by the small molecule. The proton NMR spectrum provided 255 resolved resonances that report how the explorer molecule local concentration varies with position on the surface. The measurements integrate over local dielectric constant variations, and, in principle, provide an experimental characterization of the surface free energy sampling biases introduced by the charge distribution on the protein. The experimental results for ribonuclease A obtained using positive, neutral, and negatively charged small nitroxide radicals are qualitatively similar to those expected from electrostatic calculations. However, while systematic electrostatic trends are apparent, the three different combinations of the data sets do not yield internally consistent values for the electrostatic contribution to the intermolecular free energy. We attribute this failure to the weakness of the electrostatic sampling bias for charged nitroxides in water and local variations in effective translational diffusion constant at the water-protein interface, which enters the nuclear spin relaxation equations for the nitroxide-proton dipolar coupling.
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Affiliation(s)
- Ching-Ling Teng
- Chemistry Department, Biophysics Program, University of Virginia, Charlottesville, VA 22904-4319, USA
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35
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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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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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Diakova G, Fuller Z, Victor K, Fumino K, Bryant RG. Chromium(III) complexes as intermolecular probes. JOURNAL OF MAGNETIC RESONANCE (SAN DIEGO, CALIF. : 1997) 2005; 175:65-72. [PMID: 15949749 DOI: 10.1016/j.jmr.2005.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2005] [Revised: 03/20/2005] [Accepted: 03/25/2005] [Indexed: 05/02/2023]
Abstract
Metal ion complexes provide flexible paramagnetic centers that may be used to define intermolecular contacts in a variety of solution phase environments because both the charge and electronic relaxation properties of the complex may be varied. For most complex ions, there are several proton equilibria that may change the effective charge on the complex as a function of pH which in turn affects the efficacy of application for defining the electrostatic surfaces of co-solute molecules. We report here spectrophotometric and nuclear spin relaxation studies on aqueous solutions of chromium(III) complexes of EDTA, DTPA, and bis-amides of both. The effective charges available from these paramagnetic centers range from -3 to +1 and we report the pH ranges over which the effective charge is defined with confidence for application in magnetic relaxation experiments.
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Affiliation(s)
- Galina Diakova
- Chemistry Department, University of Virginia, Charlottesville, VA 22904-4319, USA
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38
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Teng CL, Martini S, Bryant RG. Local measures of intermolecular free energies in solution. J Am Chem Soc 2005; 126:15253-7. [PMID: 15548022 DOI: 10.1021/ja0462528] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proton spin-lattice relaxation rate changes induced by freely diffusing oxygen in aqueous and mixed solvents are reported for representative amino acids and glucose. The local oxygen concentration at each spectrally resolved proton was deduced from the paramagnetic contribution to the relaxation rate. The measured relaxation increment is compared to that of the force-free diffusion relaxation model, and the differences are related to a free energy for the oxygen association with different portions of the solute molecules. The free energy differences are small, on the order of -800 to -2000 J/mol, but are uniformly negative for all proton positions measured on the amino acids in water and reflect the energetic benefit of weak association of hydrophobic cosolutes. For glucose, CH proton positions report negative free energies for oxygen association, the magnitude of which depends on the solvent; however, the hydroxyl positions report positive free energy differences relative to the force-free diffusion model, which is consistent with partial occupancy in the OH region by a solvent hydrogen bond.
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Affiliation(s)
- Ching-Ling Teng
- Chemistry Department and Biophysics Program, University of Virginia, Charlottesville, Virginia 22904, USA
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39
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Teng CL, Bryant RG. Mapping oxygen accessibility to ribonuclease a using high-resolution NMR relaxation spectroscopy. Biophys J 2004; 86:1713-25. [PMID: 14990499 PMCID: PMC1304007 DOI: 10.1016/s0006-3495(04)74240-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Paramagnetic contributions to nuclear magnetic spin-lattice relaxation rate constant induced by freely diffusing molecular oxygen measured at hundreds of different protein proton sites provide a direct means for characterizing the exploration of the protein by oxygen. This report focuses on regions of ribonuclease A where the rate constant enhancements are either quite large or quite small. We find that there are several regions of enhanced oxygen affinity for the protein both on the surface and in interior pockets where sufficient free volume permits. Oxygen has weak associative interactions with a number of surface crevices that are generally between secondary structural elements of the protein fold. Several regions near the surface have higher than expected accessibility to oxygen indicating that structural fluctuations in the protein provide intermolecular access. Oxygen penetrates part of the hydrophobic interior, but affinity does not correlate simply with hydrophobicity indices. Oxygen is excluded from regions of high interior packing density and a few surface sites where x-ray diffraction data have indicated the presence of specific hydration with high occupancy.
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Affiliation(s)
- Ching-Ling Teng
- Biophysics Program and Chemistry Department, University of Virginia, Charlottesville, Virginia 22904-4319, USA
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40
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Suzuki M, Kurimoto E, Nirasawa S, Masuda Y, Hori K, Kurihara Y, Shimba N, Kawai M, Suzuki EI, Kato K. Recombinant curculin heterodimer exhibits taste-modifying and sweet-tasting activities. FEBS Lett 2004; 573:135-8. [PMID: 15327988 DOI: 10.1016/j.febslet.2004.07.073] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2004] [Revised: 07/09/2004] [Accepted: 07/12/2004] [Indexed: 11/26/2022]
Abstract
Curculin from Curculigo latifolia is a unique sweet protein that exhibits both sweet-tasting and taste-modifying activities. We isolated a gene that encodes a novel protein highly homologous to curculin. Using cDNAs of the previously known curculin (designated as curculin1) and the novel curculin isoform (curculin2), we produced a panel of homodimeric and heterodimeric recombinant curculins by Escherichia coli expression systems. It was revealed that sweet-tasting and taste-modifying activities were exhibited solely by the heterodimer of curculin1 and curculin2.
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Affiliation(s)
- Maiko Suzuki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku, Nagoya 467-8603, Japan
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41
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Tancredi T, Pastore A, Salvadori S, Esposito V, Temussi PA. Interaction of sweet proteins with their receptor. ACTA ACUST UNITED AC 2004; 271:2231-40. [PMID: 15153113 DOI: 10.1111/j.1432-1033.2004.04154.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mechanism of interaction of sweet proteins with the T1R2-T1R3 sweet taste receptor has not yet been elucidated. Low molecular mass sweeteners and sweet proteins interact with the same receptor, the human T1R2-T1R3 receptor. The presence on the surface of the proteins of "sweet fingers", i.e. protruding features with chemical groups similar to those of low molecular mass sweeteners that can probe the active site of the receptor, would be consistent with a single mechanism for the two classes of compounds. We have synthesized three cyclic peptides corresponding to the best potential "sweet fingers" of brazzein, monellin and thaumatin, the sweet proteins whose structures are well characterized. NMR data show that all three peptides have a clear tendency, in aqueous solution, to assume hairpin conformations consistent with the conformation of the same sequences in the parent proteins. The peptide corresponding to the only possible loop of brazzein, c[CFYDEKRNLQC(37-47)], exists in solution in a well ordered hairpin conformation very similar to that of the same sequence in the parent protein. However, none of the peptides has a sweet taste. This finding strongly suggests that sweet proteins recognize a binding site different from the one that binds small molecular mass sweeteners. The data of the present work support an alternative mechanism of interaction, the "wedge model", recently proposed for sweet proteins [Temussi, P. A. (2002) FEBS Lett.526, 1-3.].
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42
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Niccolai N, Spiga O, Bernini A, Scarselli M, Ciutti A, Fiaschi I, Chiellini S, Molinari H, Temussi PA. NMR studies of protein hydration and TEMPOL accessibility. J Mol Biol 2003; 332:437-47. [PMID: 12948493 DOI: 10.1016/s0022-2836(03)00852-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the mechanisms of the interaction between a protein surface and its outer molecular environment is of primary relevance for the rational design of new drugs and engineered proteins. Protein surface accessibility is emerging as a new dimension of Structural Biology, since NMR methods have been developed to follow how molecules, even those different from physiological ligands, preferentially approach specific regions of the protein surface. Hen egg-white lysozyme, a paradigmatic example of the state of the art of protein structure and dynamics, has been selected as a model system to study protein surface accessibility. Bound water and soluble spin-labels have been used to investigate the interaction of this enzyme, both free and bound to the inhibitor (NAG)(3), with its molecular environment. No tightly bound water molecules were found inside the enzyme active site, which, conversely, appeared as the most exposed to visits from the soluble paramagnetic probe TEMPOL. From the presented set of data, an integrated view of lysozyme surface accessibility towards water and TEMPOL molecules is obtained.
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Affiliation(s)
- Neri Niccolai
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, via A. Fiorentina, I-53100, Siena, Italy.
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43
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Assadi-Porter FM, Abildgaard F, Blad H, Markley JL. Correlation of the sweetness of variants of the protein brazzein with patterns of hydrogen bonds detected by NMR spectroscopy. J Biol Chem 2003; 278:31331-9. [PMID: 12732626 DOI: 10.1074/jbc.m302663200] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
In sequence-function investigations, approaches are needed for rapidly screening protein variants for possible changes in conformation. Recent NMR methods permit direct detection of hydrogen bonds through measurements of scalar couplings that traverse hydrogen bonds (trans-hydrogen bond couplings). We have applied this approach to screen a series of five single site mutants of the sweet protein brazzein with altered sweetness for possible changes in backbone hydrogen bonding with respect to wild-type. Long range, three-dimensional data correlating connectivities among backbone 1HN, 15N, and 13C' atoms were collected from the six brazzein proteins labeled uniformly with carbon-13 and nitrogen-15. In wild-type brazzein, this approach identified 17 backbone hydrogen bonds. In the mutants, altered magnitudes of the couplings identified hydrogen bonds that were strengthened or weakened; missing couplings identified hydrogen bonds that were broken, and new couplings indicated the presence of new hydrogen bonds. Within the series of brazzein mutants investigated, a pattern was observed between sweetness and the integrity of particular hydrogen bonds. All three "sweet" variants exhibited the same pattern of hydrogen bonds, whereas all three "non-sweet" variants lacked one hydrogen bond at the middle of the alpha-helix, where it is kinked, and one hydrogen bond in the middle of beta-strands II and III, where they are twisted. Two of the non-sweet variants lack the hydrogen bond connecting the N and C termini. These variants showed greater mobility in the N- and C-terminal regions than wild-type brazzein.
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Affiliation(s)
- Fariba M Assadi-Porter
- National Magnetic Resonance Facility at Madison, Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA.
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44
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Spadaccini R, Trabucco F, Saviano G, Picone D, Crescenzi O, Tancredi T, Temussi PA. The mechanism of interaction of sweet proteins with the T1R2-T1R3 receptor: evidence from the solution structure of G16A-MNEI. J Mol Biol 2003; 328:683-92. [PMID: 12706725 DOI: 10.1016/s0022-2836(03)00346-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The mechanism by which sweet proteins elicit a response on the T1R2-T1R3 sweet taste receptor is still mostly unknown but has been so far related to the presence of "sweet fingers" on the protein surface able to interact with the same mechanism as that of low molecular mass sweeteners. In the search for the identification of sweet fingers, we have solved the solution structure of G16A MNEI, a structural mutant that shows a reduction of one order of magnitude in sweetness with respect to its parent protein, MNEI, a single-chain monellin. Comparison of the structures of wild-type monellin and its G16A mutant shows that the mutation does not affect the structure of potential glucophores but produces a distortion of the surface owing to the partial relative displacement of elements of secondary structure. These results show conclusively that sweet proteins do not possess a sweet finger and strongly support the hypothesis that the mechanism of interaction of sweet-tasting proteins with the recently identified T1R2-T1R3 GPC receptor is different from that of low molecular mass sweeteners.
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Affiliation(s)
- Roberta Spadaccini
- Dipartimento di Chimica, Università di Napoli Federico II, Via Cinthia 45, 80126 Naples, Italy
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45
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Temussi PA. Why are sweet proteins sweet? Interaction of brazzein, monellin and thaumatin with the T1R2-T1R3 receptor. FEBS Lett 2002; 526:1-4. [PMID: 12208493 DOI: 10.1016/s0014-5793(02)03155-1] [Citation(s) in RCA: 128] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Sweet tasting proteins interact with the same receptor that binds small molecular weight sweeteners, the T1R2-T1R3 G-protein coupled receptor, but the key groups on the protein surface responsible for the biological activity have not yet been identified. I propose that sweet proteins, contrary to small ligands, do not bind to the 'glutamate-like' pocket but stabilize the free form II of the T1R2-T1R3 receptor by attachment to a secondary binding site. Docking of brazzein, monellin and thaumatin with a model of the T1R2-T1R3 sweet taste receptor shows that the most likely complexes can indeed stabilize the active form of the receptor.
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46
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Peon J, Pal SK, Zewail AH. Hydration at the surface of the protein Monellin: dynamics with femtosecond resolution. Proc Natl Acad Sci U S A 2002; 99:10964-9. [PMID: 12177425 PMCID: PMC123193 DOI: 10.1073/pnas.162366099] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the femtosecond hydration dynamics of Monellin, a protein with a single tryptophan residue at its surface. Tryptophan was selectively used as a probe of the dynamics, and through monitoring of its fluorescence Stokes shift with time we obtained the hydration correlation function, which decays due to rotational and translational motions of water at the protein surface and in bulk. The decay exhibits a "bimodal" behavior with time constants of 1.3 and 16 ps, mirroring relaxation of the free/quasifree water molecules and surface-bound water layer (minimum binding energy of 1-2 kcal/mol). The observed slow decay of 16 ps for tryptophan in the native protein differs by more than an order of magnitude from that of bulk water because of the dynamical exchange in the layer. To examine the effect of unfolding, we also studied hydration dynamics when Monellin was denatured in a 6 M guanidine hydrochloride solution and obtained a totally different behavior: 3.5 and 56 ps. Comparing with the results of experiments on free tryptophan in the same concentration of the denaturing solution, we conclude that the fast component of 3.5 ps comes from bulk-type solvation in the 6 M guanidine hydrochloride. However, the absence of the 16-ps decay and appearance of the 56-ps component reflects a more "rigid solvation," which is likely to involve the motions of the protein backbone in the random-coiled state. With the help of polymer theory, this time scale is reproduced in agreement with experimental observations.
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Affiliation(s)
- Jorge Peon
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125, USA
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47
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Pintacuda G, Otting G. Identification of protein surfaces by NMR measurements with a pramagnetic Gd(III) chelate. J Am Chem Soc 2002; 124:372-3. [PMID: 11792196 DOI: 10.1021/ja016985h] [Citation(s) in RCA: 176] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Gd-diethylenetriamine pentaacetic acid-bismethylamide, Gd(DTPA-BMA), is shown to be a reagent suitable for the identification of protein surfaces. Compared to the conventionally used spin-label TEMPOL, Gd(DTPA-BMA) is a stronger relaxation agent, requiring lesser concentrations to achieve the same paramagnetic relaxation enhancement of solvent-exposed protein protons. It is also less hydrophobic and therefore less prone to specific binding to proteins. Relaxation enhancements predicted by a second-sphere interaction model correlated with experimental data recorded with ubiquitin, while the correlation with corresponding data recorded with TEMPOL was poor.
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Affiliation(s)
- Guido Pintacuda
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Tomtebodavägen 6, S-171 77 Stockholm, Sweden
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48
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Niccolai N, Ciutti A, Spiga O, Scarselli M, Bernini A, Bracci L, Di Maro D, Dalvit C, Molinari H, Esposito G, Temussi PA. NMR studies of protein surface accessibility. J Biol Chem 2001; 276:42455-61. [PMID: 11546818 DOI: 10.1074/jbc.m107387200] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Characterization of protein surface accessibility represents a new frontier of structural biology. A surface accessibility investigation for two structurally well-defined proteins, tendamistat and bovine pancreatic trypsin inhibitor, is performed here by a combined analysis of water-protein Overhauser effects and paramagnetic perturbation profiles induced by the soluble spin-label 4-hydroxy-2,2,6,6-tetramethyl-piperidine-1-oxyl on NMR spectra. This approach seems to be reliable not only for distinguishing between buried and exposed residues but also for finding molecular locations where a network of more ordered waters covers the protein surface. From the presented set of data, an overall picture of the surface accessibility of the two proteins can be inferred. Detailed knowledge of protein accessibility can form the basis for successful design of mutants with increased activity and/or greater specificity.
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Affiliation(s)
- N Niccolai
- Biomolecular Structure Research Center and Department of Molecular Biology, University of Siena, I-53100 Siena, Italy
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