scholarly journals Hydrogen bonding changes of internal water molecules in rhodopsin during metarhodopsin I and metarhodopsin II formation

1998 ◽  
Vol 329 (3) ◽  
pp. 713-717 ◽  
Author(s):  
Parshuram RATH ◽  
Frank DELANGE ◽  
J. Willem DEGRIP ◽  
J. Kenneth ROTHSCHILD
Keyword(s):  
Hydrogen Bonding ◽  
Conformational Changes ◽  
Structural Changes ◽  
Integral Membrane Protein ◽  
Water Molecules ◽  
Rod Outer Segments ◽  
Oh Groups ◽  
Protein Conformational Changes ◽  
Hydrogen Deuterium ◽  
Fourier Transform Ir

Rhodopsin is a 7-helix, integral membrane protein found in the rod outer segments, which serves as the light receptor in vision. Light absorption by the retinylidene chromophore of rhodopsin triggers an 11-cis → all-trans isomerization, followed by a series of protein conformational changes, which culminate in the binding and activation of the G-protein transducin by the metarhodopsin II (Meta II) intermediate. Fourier transform IR difference spectroscopy has been used to investigate the structural changes that water, as well as other OH- and NH-containing groups, undergo during the formation of the metarhodopsin I (Meta I) and Meta II intermediates. Bands associated with the OH stretch modes of water are identified by characteristic downshifts upon substitution of H218O for H2O. Compared with earlier work, several negative bands associated with water molecules in unphotolysed rhodopsin were detected, which shift to lower frequencies upon formation of the Meta I and Meta II intermediates. These data indicate that at least one water molecule undergoes an increase in hydrogen bonding upon formation of the Meta I intermediate, while at least one other increases its hydrogen bonding during Meta II formation. Amino acid residue Asp-83, which undergoes a change in its hydrogen bonding during Meta II formation, does not appear to interact with any of the structurally active water molecules. Several NH and/or OH groups, which are inaccessible to hydrogen/deuterium exchange, also undergo alterations during Meta I and Meta II formation.

Structural changes of water molecules during photoelectrochemical water oxidation on TiO2 thin film electrodes

2018 ◽  
Vol 20 (5) ◽  
pp. 3388-3394 ◽  
Author(s):  
Chandana Sampath Kumara Ranasinghe ◽  
Akira Yamakata
Keyword(s):  
Thin Film ◽  
Hydrogen Bonding ◽  
Water Oxidation ◽  
Structural Changes ◽  
Tio2 Thin Film ◽  
Water Molecules ◽  
Hydrogen Bonding Networks ◽  
Thin Film Electrodes ◽  
Photoelectrochemical Water Oxidation

Hydrogen bonding networks at the water/TiO2 interface were heavily disrupted and an isolated OH band appeared during photoelectrochemical water oxidation.

scholarly journals Role of Water Mediated Interactions in Calcium-Coupled Allostery of Calmodulin Domains

2019 ◽  
Author(s):  
Cheng Tan ◽  
Wenfei Li ◽  
Wei Wang ◽  
Dave Thirumalai
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Structural Response ◽  
Coordination Mechanism ◽  
Water Molecules ◽  
Hydrophobic Core ◽  
Physiological Importance ◽  
Allosteric Communication ◽  
Allosteric Transitions ◽  
Ef Hands

AbstractAllosteric communication between distant parts of protein controls many cellular functions. Binding of Ca2+ to the helix-loop-helix motifs (termed EF-hands) in calmodulin (CaM) leads to large conformational changes poising it for the binding of target proteins involved in variety of cell signaling events. Despite the physiological importance, the mechanism of Ca2+-mediated allosteric transitions in CaM remains elusive. Particularly, it is still unclear how water molecules contribute to Ca2+ coordination and the coupled conformational motions. We use all-atom molecular dynamics simulations with enhanced sampling method to investigate the coupling between the Ca2+ binding, dehydration, and the conformational change of the isolated CaM domains, each containing two EF-hands. We reveal a water-bridged coordination mechanism during Ca2+ binding and dehydration, in which the bridging water molecules reduce the entropy penalty during the coordination of liganding residues, thus contributing to efficient ligand binding in CaM domains. Exposure of hydrophobic sites occurs by calcium induced rotation of the helices of EF-hands with the hydrophobic core serving as the pivot. Interestingly, we find that despite being structurally similar, the structural response in the two EF-hands upon Ca2+ binding is highly asymmetric, which is needed for allosteric communication between them. The atomically detailed picture for the allosteric transitions of the CaM EF-hands, which are the first events in mediating a variety of intracellular processes, reveal the complex interplay between the discrete water molecules, dehydration of Ca2+, and CaM structural changes.Table of Contents graphic

scholarly journals The relation between intrinsic protein conformational changes and ligand binding

2020 ◽  
Author(s):  
Marijn de Boer
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Conformational Equilibrium ◽  
Biological Function ◽  
Free Protein ◽  
Classical Statistical Mechanics ◽  
Protein Conformational Changes ◽  
Ligand Free ◽  
Non Covalent Interactions ◽  
Covalent Interactions

1ABSTRACTStructural changes in proteins allow them to exist in several conformations. Non-covalent interactions with ligands drive the structural changes, thereby allowing the protein to perform its biological function. Recent findings suggest that many proteins are always in an equilibrium of different conformations and that each of these conformations can be formed by both the ligand-free and ligand-bound protein. By using classical statistical mechanics, we derived the equilibrium probabilities of forming a conformation with and without ligand. We found, under certain conditions, that increasing the probability of forming a conformation by the ligand-free protein also increases the probability of forming the same conformation when the protein has a ligand bound. Further, we found that changes in the conformational equilibrium of the ligand-free protein can increase or decrease the affinity for the ligand.

scholarly journals Adsorption and Dehydration of Water Molecules from α, β and γ Cyclodextrins — A Study by TGA Analysis and Gravimetry

2015 ◽  
Vol 1120-1121 ◽  
pp. 886-890
Author(s):  
Alfred A. Christy
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Thermogravimetric Analysis ◽  
Bond Formation ◽  
The Other ◽  
Water Molecules ◽  
Hydrogen Bond Formation ◽  
Oh Groups ◽  
Hydrogen Bondings ◽  
Tga Analysis

The adsorption and desorption of water molecules from α, β and γ-cyclodextrins were studied by gravimetric and thermogravimetric analysis. Cyclodextrins like all the other carbohydrates have tendency to adsorb water molecules. However, their cyclic nature tends to affect the adsorption patterns. The cyclic nature of the cyclodextrins facilitates the formation of hydrogen bondings between OH groups of the neighbouring glucose units. The C2(1)-OH forms hydrogen bonding with C3(2)-OH. The extent of the hydrogen bond formation and strength of the hydrogen bond affect the way the adsorption and dehydration of water molecules from cyclodextrins take place.

scholarly journals Aquaporins: More Than Functional Monomers in a Tetrameric Arrangement

Cells ◽  
2018 ◽  
Vol 7 (11) ◽  
pp. 209 ◽  
Author(s):  
Marcelo Ozu ◽  
Luciano Galizia ◽  
Cynthia Acuña ◽  
Gabriela Amodeo
Keyword(s):  
Conformational Changes ◽  
Regulatory Mechanisms ◽  
Water Molecules ◽  
Complex Structures ◽  
Functional Monomers ◽  
Water Permeation ◽  
Protein Conformational Changes ◽  
Experimental Approaches ◽  
Dynamics Simulations ◽  
Pore Lining

Aquaporins (AQPs) function as tetrameric structures in which each monomer has its own permeable pathway. The combination of structural biology, molecular dynamics simulations, and experimental approaches has contributed to improve our knowledge of how protein conformational changes can challenge its transport capacity, rapidly altering the membrane permeability. This review is focused on evidence that highlights the functional relationship between the monomers and the tetramer. In this sense, we address AQP permeation capacity as well as regulatory mechanisms that affect the monomer, the tetramer, or tetramers combined in complex structures. We therefore explore: (i) water permeation and recent evidence on ion permeation, including the permeation pathway controversy—each monomer versus the central pore of the tetramer—and (ii) regulatory mechanisms that cannot be attributed to independent monomers. In particular, we discuss channel gating and AQPs that sense membrane tension. For the latter we propose a possible mechanism that includes the monomer (slight changes of pore shape, the number of possible H-bonds between water molecules and pore-lining residues) and the tetramer (interactions among monomers and a positive cooperative effect).

Protein-induced conformational changes in 16S rRNA during assembly of the Escherichia Coli 30S ribosomal subunit: A STEM study

1987 ◽  
Vol 45 ◽  
pp. 910-911
Author(s):  
M. Boublik ◽  
V. Mandiyan ◽  
J.F. Hainfeld ◽  
J.S. Wall
Keyword(s):  
16S Rrna ◽  
Conformational Changes ◽  
Ribosomal Proteins ◽  
Structural Changes ◽  
Ribosomal Subunit ◽  
Compact Structure ◽  
E Coli ◽  
Freeze Dried ◽  
16S Rna ◽  
30S Subunit

The aim of this study is to understand the mechanism of 16S rRNA folding into the compact structure of the small 30S subunit of E. coli ribosome. The assembly of the 30S E. coli ribosomal subunit is a sequence of specific interactions of 16S rRNA with 21 ribosomal proteins (S1-S21). Using dedicated high resolution STEM we have monitored structural changes induced in 16S rRNA by the proteins S4, S8, S15 and S20 which are involved in the initial steps of 30S subunit assembly. S4 is the first protein to bind directly and stoichiometrically to 16S rRNA. Direct binding also occurs individually between 16S RNA and S8 and S15. However, binding of S20 requires the presence of S4 and S8. The RNA-protein complexes are prepared by the standard reconstitution procedure, dialyzed against 60 mM KCl, 2 mM Mg(OAc)2, 10 mM-Hepes-KOH pH 7.5 (Buffer A), freeze-dried and observed unstained in dark field at -160°.

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