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Lameiras P, Nuzillard JM. Tailoring the nuclear Overhauser effect for the study of small and medium-sized molecules by solvent viscosity manipulation. PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY 2021; 123:1-50. [PMID: 34078536 DOI: 10.1016/j.pnmrs.2020.12.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/06/2020] [Accepted: 12/02/2020] [Indexed: 06/12/2023]
Abstract
The nuclear Overhauser effect (NOE) is a consequence of cross-relaxation between nuclear spins mediated by dipolar coupling. Its sensitivity to internuclear distances has made it an increasingly important tool for the determination of through-space atom proximity relationships within molecules of sizes ranging from the smallest systems to large biopolymers. With the support of sophisticated FT-NMR techniques, the NOE plays an essential role in structure elucidation, conformational and dynamic investigations in liquid-state NMR. The efficiency of magnetization transfer by the NOE depends on the molecular rotational correlation time, whose value depends on solution viscosity. The magnitude of the NOE between 1H nuclei varies from +50% when molecular tumbling is fast to -100% when it is slow, the latter case corresponding to the spin diffusion limit. In an intermediate tumbling regime, the NOE may be vanishingly small. Increasing the viscosity of the solution increases the motional correlation time, and as a result, otherwise unobservable NOEs may be revealed and brought close to the spin diffusion limit. The goal of this review is to report the resolution of structural problems that benefited from the manipulation of the negative NOE by means of viscous solvents, including examples of molecular structure determination, conformation elucidation and mixture analysis (the ViscY method).
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Affiliation(s)
- Pedro Lameiras
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
| | - Jean-Marc Nuzillard
- Université de Reims Champagne-Ardenne, CNRS, ICMR UMR 7312, 51097 Reims, France
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2
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Her C, Yeh Y, Krishnan VV. The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy. Biomolecules 2019; 9:biom9060235. [PMID: 31213033 PMCID: PMC6628104 DOI: 10.3390/biom9060235] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 05/28/2019] [Accepted: 05/30/2019] [Indexed: 12/13/2022] Open
Abstract
The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.
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Affiliation(s)
- Cheenou Her
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
| | - Yin Yeh
- Department of Applied Science, University of California, Davis, CA 95616, USA.
| | - Viswanathan V Krishnan
- Department of Chemistry, California State University, Fresno, CA 93740, USA.
- Department Medical Pathology and Laboratory Medicine, Davis School of Medicine, University of California, Davis, CA 95616, USA.
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3
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Nesmelova IV, Melnikova DL, Ranjan V, Skirda VD. Translational diffusion of unfolded and intrinsically disordered proteins. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 166:85-108. [PMID: 31521238 DOI: 10.1016/bs.pmbts.2019.05.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Translational (or self-diffusion) coefficient in dilute solution is inversely proportional to the size of a diffusing molecule, and hence self-diffusion coefficient measurements have been applied to determine the effective hydrodynamic radii for a range of native and nonnative protein conformations. In particular, translational diffusion coefficient measurements are useful to estimate the hydrodynamic radius of natively (or intrinsically) disordered proteins in solution, and, thereby, probe the compactness of a protein as well as its change when environmental parameters such as temperature, solution pH, or protein concentration are varied. The situation becomes more complicated in concentrated solutions. In this review, we discuss the translational diffusion of disordered proteins in dilute and crowded solutions, focusing primarily on the information provided by pulsed-field gradient NMR technique, and draw analogies to well-structured globular proteins and synthetic polymers.
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Affiliation(s)
- Irina V Nesmelova
- Department of Physics and Optical Sciences, University of North Carolina, Charlotte, NC, United States; Center for Biomedical Engineering and Science, University of North Carolina, Charlotte, NC, United States.
| | | | - Venkatesh Ranjan
- Department of Chemistry, University of North Carolina, Charlotte, NC, United States
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4
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Abstract
Antifreeze glycoproteins are an important class of biological antifreezes that have potential applications in many areas of medicine, agriculture and industry in which ice crystal growth is damaging. While the synthesis of antifreeze glycoproteins as pure glycoforms has recently been achieved by using ligation and polymerisation strategies, the routine production of large quantities of pure glycoforms remains challenging. A range of C-linked analogues that are readily produced by solid-phase synthesis have delivered novel compounds that are not biological antifreezes, but are potent, non-cytotoxic, ice-recrystallisation inhibitors. Structure-activity studies, the identification of cyclic antifreeze glycoproteins and conformational studies have provided further insight into the requirements for antifreeze activity. These results, coupled with significant advances in approaches to the routine synthesis of different glycoproteins and mimics, present opportunities for the design and synthesis of novel ice-growth-inhibiting and antifreeze compounds.
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Affiliation(s)
- James Garner
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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5
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Peltier R, Brimble MA, Wojnar JM, Williams DE, Evans CW, DeVries AL. Synthesis and antifreeze activity of fish antifreeze glycoproteins and their analogues. Chem Sci 2010. [DOI: 10.1039/c0sc00194e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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6
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Uda Y, Zepeda S, Kaneko F, Matsuura Y, Furukawa Y. Adsorption-Induced Conformational Changes of Antifreeze Glycoproteins at the Ice/Water Interface. J Phys Chem B 2007; 111:14355-61. [DOI: 10.1021/jp075429s] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yukihiro Uda
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Salvador Zepeda
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Fumitoshi Kaneko
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshiki Matsuura
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
| | - Yoshinori Furukawa
- Institute of Low Temperature Science, Hokkaido University, Kita-19, Nishi-8, Kita-ku, Sapporo 060-0819, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 560-0043, and Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
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7
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Younes-Metzler O, Ben RN, Giorgi JB. Pattern formation of antifreeze glycoproteins via solvent evaporation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2007; 23:11355-11359. [PMID: 17927221 DOI: 10.1021/la701408m] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Surface patterning of antifreeze glycoprotein fraction 8 (AFGP 8) via a solvent evaporation method is reported here. In this process, lines of AFGP 8 particles and gridlike patterns were formed as as result of the receding of the droplet contact line and the accumulation of the solute during evaporation. The solution concentration strongly affects the protein line spacing. The average height of the protein was measured to be 8.1 +/- 2.5 A, which may be attributed to the height of a single molecule.
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Affiliation(s)
- Osnat Younes-Metzler
- Center for Catalysis Research and Innovation, University of Ottawa, 10 Marie Curie Street, Ottawa, Ontario, Canada K1N 6N5
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8
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Inglis SR, McGann MJ, Price WS, Harding MM. Diffusion NMR studies on fish antifreeze proteins and synthetic analogues. FEBS Lett 2006; 580:3911-5. [PMID: 16797544 DOI: 10.1016/j.febslet.2006.06.022] [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: 05/21/2006] [Revised: 06/01/2006] [Accepted: 06/07/2006] [Indexed: 10/24/2022]
Abstract
Pulsed field gradient spin echo NMR spectroscopy was used to measure diffusion coefficients of the alpha-helical type I antifreeze protein from the winter flounder, two synthetic derivatives in which the four Thr residues were replaced with Val and Ala, respectively, and the low molecular weight fraction antifreeze glycoprotein. Under the conditions studied, the natural type I antifreeze protein and low molecular weight glycoprotein gave diffusion values that were consistent with the presence of monomeric protein in solution. While significant aggregation of the Ala analogue was observed (2-10 mM), there was no evidence for aggregation in the Val analogue (1-3 mM). These results are compared with previously reported solubility and thermal hysteresis data and the implications for the design of synthetic antifreeze proteins are discussed.
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Affiliation(s)
- Steven R Inglis
- School of Chemistry, The University of New South Wales, Sydney, NSW 2052, Australia
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9
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Bouvet VR, Lorello GR, Ben RN. Aggregation of antifreeze glycoprotein fraction 8 and its effect on antifreeze activity. Biomacromolecules 2006; 7:565-71. [PMID: 16471931 DOI: 10.1021/bm050605t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Antifreeze glycoproteins (AFGPs) have many potential applications ranging from the cryopreservation and hypothermic storage of tissues and organs to the preservation of various frozen food products. Since supplying native AFGP for these applications is a labor-intensive and costly process, the rational design and synthesis of functional AFGP analogues is a very attractive alternative. While structure-function studies have implicated specific structural motifs as essential for antifreeze activity in AFGP, the relationship between solution conformation and antifreeze activity is poorly understood. Toward this end, we have analyzed AFGP8 in aqueous solutions using dynamic light scattering (DLS) and circular dichroism (CD). Our results indicate that AFGP8 forms discrete aggregates in solution. These aggregates are predominantly composed of dimers that form at solution concentrations greater than 20 mM. CD spectroscopy indicates that the preferred solution conformation of AFGP8 is consistent with that of random coil. However, significant beta-sheet and alpha-helix character is observed in more concentrated solutions, indicating that these glycopeptides are highly flexible in solution. Aggregation appears to have a minimal effect on the overall solution conformation. Thermal hysteresis (TH) activity of the aggregated solutions is much higher than that of less concentrated solutions that do not form aggregates. While cooperative functioning between lower and higher molecular weight AFGPs has been reported, this is the first instance where cooperative functioning in lower molecular weight AFGPs has been observed.
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Affiliation(s)
- Vincent R Bouvet
- Department of Chemistry, 10 Marie Curie, University of Ottawa, Ottawa, Ontario, Canada K1N 6N5
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10
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Krishnan VV, Lau EY, Tsvetkova NM, Feeney RE, Fink WH, Yeh Y. Characterization of the restricted rotation of the dimethyl groups in chemically N-terminal 13C-labeled antifreeze glycoproteins: a temperature-dependent study in water to ice through the supercooled state. J Chem Phys 2005; 123:044702. [PMID: 16095379 DOI: 10.1063/1.1924549] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Site-specific chemical modification, especially with isotopically enriched groups, allows one to study the structure and dynamics of proteins for which uniform enrichment is difficult. When the N-terminal alanine in antifreeze glycoprotein (AFGP) is replaced with an N,N-dimethyl alanine the methyl groups show signatures of slow rotation about the C-N bond. In order to separate the local dynamics of the N-terminus from the overall protein dynamics, we present a complete characterization of this dynamics. Temperature-dependent nuclear magnetic-resonance experiments from room temperature to subzero temperatures, including the supercooled state and in the presence of ice, are presented. Quantum chemical calculations are also performed on a localized N-terminus of the AFGP. Our results show that in the solution state at room temperature and in the super cooled regime, the dimethyl groups undergo a slow, restricted rotation with an unequal distribution of population between two major conformations. At lower temperatures in the presence of ice, the dynamics become much more complex due to freezing out of several conformational states. Based on these results, we conclude that the segmental dynamics of the N-terminus are local to the first residue and do not affect the overall dynamics of the protein.
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Affiliation(s)
- V V Krishnan
- Bioscience Directorate, Lawrence Livermore National Laboratory, Livermore, California 94551, USA.
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