scholarly journals Dynamics and mechanism of ultrafast water–protein interactions

2016 ◽  
Vol 113 (30) ◽  
pp. 8424-8429 ◽  
Author(s):  
Yangzhong Qin ◽  
Lijuan Wang ◽  
Dongping Zhong
Keyword(s):  
Protein Interactions ◽  
Hydration Shell ◽  
Water Dynamics ◽  
Side Chain ◽  
Water Molecules ◽  
Ultrafast Dynamics ◽  
Hydration Water ◽  
Water Side ◽  
Dynamics And Function ◽  
And Function

Protein hydration is essential to its structure, dynamics, and function, but water–protein interactions have not been directly observed in real time at physiological temperature to our awareness. By using a tryptophan scan with femtosecond spectroscopy, we simultaneously measured the hydration water dynamics and protein side-chain motions with temperature dependence. We observed the heterogeneous hydration dynamics around the global protein surface with two types of coupled motions, collective water/side-chain reorientation in a few picoseconds and cooperative water/side-chain restructuring in tens of picoseconds. The ultrafast dynamics in hundreds of femtoseconds is from the outer-layer, bulk-type mobile water molecules in the hydration shell. We also found that the hydration water dynamics are always faster than protein side-chain relaxations but with the same energy barriers, indicating hydration shell fluctuations driving protein side-chain motions on the picosecond time scales and thus elucidating their ultimate relationship.

Conformational stability, dynamics and function of human frataxin: Tryptophan side chain interplay

2021 ◽  
pp. 109086
Author(s):  
Lucía D. Espeche ◽  
Karl Ellioth Sewell ◽  
Ignacio H. Castro ◽  
Luciana Capece ◽  
María Florencia Pignataro ◽  
...  
Keyword(s):  
Conformational Stability ◽  
Side Chain ◽  
Dynamics And Function ◽  
Stability Dynamics ◽  
And Function

scholarly journals Water–protein interactions from high–resolution protein crystallography

2004 ◽  
Vol 359 (1448) ◽  
pp. 1191-1206 ◽  
Author(s):  
Masayoshi Nakasako
Keyword(s):  
Hydrogen Bond ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Water Molecules ◽  
Aqueous Environment ◽  
Hydration Water ◽  
X Ray Crystallography ◽  
Physico Chemical ◽  
Domain Motions

To understand the role of water in life at molecular and atomic levels, structures and interactions at the protein–water interface have been investigated by cryogenic X–ray crystallography. The method enabled a much clearer visualization of definite hydration sites on the protein surface than at ambient temperature. Using the structural models of proteins, including several hydration water molecules, the characteristics in hydration structures were systematically analysed for the amount, the interaction geometries between water molecules and proteins, and the local and global distribution of water molecules on the surface of proteins. The tetrahedral hydrogen–bond geometry of water molecules in bulk solvent was retained at the interface and enabled the extension of a three–dimensional chain connection of a hydrogen–bond network among hydration water molecules and polar protein atoms over the entire surface of proteins. Networks of hydrogen bonds were quite flexible to accommodate and/or to regulate the conformational changes of proteins such as domain motions. The present experimental results may have profound implications in the understanding of the physico–chemical principles governing the dynamics of proteins in an aqueous environment and a discussion of why water is essential to life at a molecular level.

scholarly journals Site-specific glycosylation regulates the form and function of the intermediate filament cytoskeleton

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Heather J Tarbet ◽  
Lee Dolat ◽  
Timothy J Smith ◽  
Brett M Condon ◽  
E Timothy O'Brien ◽  
...  
Keyword(s):  
Protein Interactions ◽  
Transferase Activity ◽  
Protein Protein Interactions ◽  
Site Specific ◽  
Form And Function ◽  
Glycosylation Sites ◽  
Wide Range ◽  
Dynamics And Function ◽  
Glcnac Transferase ◽  
And Function

Intermediate filaments (IF) are a major component of the metazoan cytoskeleton and are essential for normal cell morphology, motility, and signal transduction. Dysregulation of IFs causes a wide range of human diseases, including skin disorders, cardiomyopathies, lipodystrophy, and neuropathy. Despite this pathophysiological significance, how cells regulate IF structure, dynamics, and function remains poorly understood. Here, we show that site-specific modification of the prototypical IF protein vimentin with O-linked β-N-acetylglucosamine (O-GlcNAc) mediates its homotypic protein-protein interactions and is required in human cells for IF morphology and cell migration. In addition, we show that the intracellular pathogen Chlamydia trachomatis, which remodels the host IF cytoskeleton during infection, requires specific vimentin glycosylation sites and O-GlcNAc transferase activity to maintain its replicative niche. Our results provide new insight into the biochemical and cell biological functions of vimentin O-GlcNAcylation, and may have broad implications for our understanding of the regulation of IF proteins in general.

scholarly journals Water-Protein Interactions: The Secret of Protein Dynamics

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Silvia Martini ◽  
Claudia Bonechi ◽  
Alberto Foletti ◽  
Claudio Rossi
Keyword(s):  
Protein Interactions ◽  
Nmr Relaxation ◽  
Spin Lattice Relaxation ◽  
Resonance Spectroscopy ◽  
Water Molecules ◽  
Hydration Water ◽  
Relaxation Rates ◽  
Relaxation Parameters ◽  
Hydration Shells ◽  
Dynamical Properties

Water-protein interactions help to maintain flexible conformation conditions which are required for multifunctional protein recognition processes. The intimate relationship between the protein surface and hydration water can be analyzed by studying experimental water properties measured in protein systems in solution. In particular, proteins in solution modify the structure and the dynamics of the bulk water at the solute-solvent interface. The ordering effects of proteins on hydration water are extended for several angstroms. In this paper we propose a method for analyzing the dynamical properties of the water molecules present in the hydration shells of proteins. The approach is based on the analysis of the effects of protein-solvent interactions on water protons NMR relaxation parameters. NMR relaxation parameters, especially the nonselective (R1NS) and selective (R1SE) spin-lattice relaxation rates of water protons, are useful for investigating the solvent dynamics at the macromolecule-solvent interfaces as well as the perturbation effects caused by the water-macromolecule interactions on the solvent dynamical properties. In this paper we demonstrate that Nuclear Magnetic Resonance Spectroscopy can be used to determine the dynamical contributions of proteins to the water molecules belonging to their hydration shells.

The organization and function of water in protein crystals

1977 ◽  
Vol 278 (959) ◽  
pp. 3-32 ◽  
Keyword(s):  
Protein Interactions ◽  
Active Sites ◽  
Structural Integrity ◽  
Bound Water ◽  
Structural Data ◽  
Protein Molecule ◽  
Biologically Active ◽  
Complex Nature ◽  
Water Molecules ◽  
And Function

Dry proteins are dead, or at best asleep. Substitution of D 2 O can drastically alter biological activity. Water is thus essential in maintaining the structural integrity of biologically active macromolecules, and is implicated in their functioning. Such water may occupy a range of dynamical states, from being strongly bound and localized, to more labile and ‘liquid-like’. Spatially ordering the macromolecules aids the search for the more localized water molecules. For example, diffraction experiments on single crystals can resolve ‘bound’ water molecules within a protein molecule - often at active sites, coordinated to metals or ions. Less precise information is obtained on the partially occupied external water sites, which are of importance to the folding and the dynamics of the biomolecule. Orientation of fibrous molecules increases the information obtainable from n.m.r. experiments. Combination of other experimental results on disordered aggregates (e.g. in solution) with chemical and structural data on the macromolecule and water itself yields useful, if circumstantial, information. Statistical and computer techniques may help to elucidate the complex nature of water-protein interactions, and to interpret the results of more complex experiments.

WatAA: Atlas of Protein Hydration. Exploring synergies between data mining and ab initio calculations

2017 ◽  
Vol 19 (26) ◽  
pp. 17094-17102 ◽  
Author(s):  
Jiří Černý ◽  
Bohdan Schneider ◽  
Lada Biedermannová
Keyword(s):  
Data Mining ◽  
Protein Structure ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Protein Hydration ◽  
Water Molecules ◽  
Structure Dynamics ◽  
Dynamics And Function ◽  
And Function

Water molecules represent an integral part of proteins and a key determinant of protein structure, dynamics and function.

scholarly journals Trapped water molecules are essential to structural dynamics and function of a ribozyme

2006 ◽  
Vol 103 (36) ◽  
pp. 13380-13385 ◽  
Author(s):  
M. M. Rhodes ◽  
K. Reblova ◽  
J. Sponer ◽  
N. G. Walter
Keyword(s):  
Structural Dynamics ◽  
Water Molecules ◽  
Dynamics And Function ◽  
And Function

Formation and Function of Formate in the Side-Chain Alkylation of Toluene with Methanol

2013 ◽  
Vol 33 (6) ◽  
pp. 1041-1047
Author(s):  
Dan LIN ◽  
Huimin ZHAO ◽  
Xiaoyue ZHANG ◽  
Dongxue LAN ◽  
Yuan CHUN
Keyword(s):  
Side Chain ◽  
And Function

Ecosystems processes

2018 ◽  
Author(s):  
Karen J. Esler ◽  
Anna L. Jacobsen ◽  
R. Brandon Pratt
Keyword(s):  
Ecosystem Function ◽  
Mineral Nutrients ◽  
Structure And Function ◽  
Water Dynamics ◽  
Ecosystem Level ◽  
Key Drivers ◽  
And Function ◽  
Mediterranean Type Ecosystems

Ecosystems are assemblages of organisms interacting with one another and their environment (Chapter 1). Key to the functioning of ecosystems is the flow of energy, carbon, mineral nutrients, and water in these systems. The numerous processes involved are chiefly driven by climate, soil, and fire (Chapter 2). In cases where the key drivers are the same in different areas, then ecosystems should converge in their structure and function, which has been a motivation for comparing across mediterranean-type climate (MTC) regions. Convergence of MTC regions has been evaluated, but such comparisons at the ecosystem level are challenging because ecosystems are complex and dynamic entities. Here we review carbon, nutrient, and water dynamics of mediterranean-type ecosystems in the context of ecosystem function. As nutrients in soils are low in some MTC regions, we review how this has led to unique adaptations to meet this challenge.

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