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 Mass Spectrometry and Structural Biology Techniques in the Studies on the Coronavirus-Receptor Interaction

Molecules ◽  
2020 ◽  
Vol 25 (18) ◽  
pp. 4133
Author(s):  
Danuta Witkowska
Keyword(s):  
Mass Spectrometry ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Three Dimensional ◽  
Cell Receptor ◽  
Receptor Protein ◽  
Receptor Interaction ◽  
S Protein ◽  
X Ray Crystallography ◽  
Huge Impact

Mass spectrometry and some other biophysical methods, have made substantial contributions to the studies on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and human proteins interactions. The most interesting feature of SARS-CoV-2 seems to be the structure of its spike (S) protein and its interaction with the human cell receptor. Mass spectrometry of spike S protein revealed how the glycoforms are distributed across the S protein surface. X-ray crystallography and cryo-electron microscopy made huge impact on the studies on the S protein and ACE2 receptor protein interaction, by elucidating the three-dimensional structures of these proteins and their conformational changes. The findings of the most recent studies in the scope of SARS-CoV-2-Human protein-protein interactions are described here.

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.

scholarly journals Crystal structure and hydrogen bonding in the water-stabilized proton-transfer salt brucinium 4-aminophenylarsonate tetrahydrate

2016 ◽  
Vol 72 (5) ◽  
pp. 751-755 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Network Structure ◽  
Three Dimensional ◽  
Water Molecules ◽  
Arsanilic Acid ◽  
Dimensional Network

In the structure of the brucinium salt of 4-aminophenylarsonic acid (p-arsanilic acid), systematically 2,3-dimethoxy-10-oxostrychnidinium 4-aminophenylarsonate tetrahydrate, (C23H27N2O4)[As(C6H7N)O2(OH)]·4H2O, the brucinium cations form the characteristic undulating and overlapping head-to-tail layered brucine substructures packed along [010]. The arsanilate anions and the water molecules of solvation are accommodated between the layers and are linked to them through a primary cation N—H...O(anion) hydrogen bond, as well as through water O—H...O hydrogen bonds to brucinium and arsanilate ions as well as bridging water O-atom acceptors, giving an overall three-dimensional network structure.

(NH4)[B3PO6(OH)3]·0.5H2O

2007 ◽  
Vol 63 (11) ◽  
pp. i185-i185 ◽  
Author(s):  
Wei Liu ◽  
Jingtai Zhao
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bond ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Hydrogen Bond Network ◽  
Ammonium Ions ◽  
One Dimensional ◽  
Bond Network ◽  
Solvothermal Conditions

The title compound, ammonium catena-[monoboro-monodihydrogendiborate-monohydrogenphosphate] hemihydrate, was obtained under solvothermal conditions using glycol as the solvent. The crystal structure is constructed of one-dimensional infinite borophosphate chains, which are interconnected by ammonium ions and water molecules via a complex hydrogen-bond network to form a three-dimensional structure. The water molecules of crystallization are disordered over inversion centres, and their H atoms were not located.

scholarly journals Chemical Decorations of “MARs” Residents in Orchestrating Eukaryotic Gene Regulation

2020 ◽  
Vol 8 ◽  
Author(s):  
Tanaya Roychowdhury ◽  
Samit Chattopadhyay
Keyword(s):  
Gene Regulation ◽  
Conformational Changes ◽  
Protein Interactions ◽  
Protein Function ◽  
Functional Outcomes ◽  
Three Dimensional ◽  
Limited Information ◽  
Post Translational Modification ◽  
Cellular Functions ◽  
3D Matrix

Genome organization plays a crucial role in gene regulation, orchestrating multiple cellular functions. A meshwork of proteins constituting a three-dimensional (3D) matrix helps in maintaining the genomic architecture. Sequences of DNA that are involved in tethering the chromatin to the matrix are called scaffold/matrix attachment regions (S/MARs), and the proteins that bind to these sequences and mediate tethering are termed S/MAR-binding proteins (S/MARBPs). The regulation of S/MARBPs is important for cellular functions and is altered under different conditions. Limited information is available presently to understand the structure–function relationship conclusively. Although all S/MARBPs bind to DNA, their context- and tissue-specific regulatory roles cannot be justified solely based on the available information on their structures. Conformational changes in a protein lead to changes in protein–protein interactions (PPIs) that essentially would regulate functional outcomes. A well-studied form of protein regulation is post-translational modification (PTM). It involves disulfide bond formation, cleavage of precursor proteins, and addition or removal of low-molecular-weight groups, leading to modifications like phosphorylation, methylation, SUMOylation, acetylation, PARylation, and ubiquitination. These chemical modifications lead to varied functional outcomes by mechanisms like modifying DNA–protein interactions and PPIs, altering protein function, stability, and crosstalk with other PTMs regulating subcellular localizations. S/MARBPs are reported to be regulated by PTMs, thereby contributing to gene regulation. In this review, we discuss the current understanding, scope, disease implications, and future perspectives of the diverse PTMs regulating functions of S/MARBPs.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

One-dimensional CuIIcoordination polymers containingC2h-symmetric 1,1′:4′,1′′-terphenyl-3,3′-dicarboxylate linkers

2015 ◽  
Vol 71 (10) ◽  
pp. 929-935 ◽  
Author(s):  
Hyun-Chul Kim ◽  
Ja-Min Gu ◽  
Seong Huh ◽  
Chul-Hyun Yo ◽  
Youngmee Kim
Keyword(s):  
Coordination Polymers ◽  
Three Dimensional ◽  
Polymer Chains ◽  
Water Molecules ◽  
Binding Modes ◽  
Bridging Ligands ◽  
One Dimensional ◽  
X Ray Crystallography ◽  
Dimensional Network ◽  
The One

Two new one-dimensional CuIIcoordination polymers (CPs) containing theC2h-symmetric terphenyl-based dicarboxylate linker 1,1′:4′,1′′-terphenyl-3,3′-dicarboxylate (3,3′-TPDC), namelycatena-poly[[bis(dimethylamine-κN)copper(II)]-μ-1,1′:4′,1′′-terphenyl-3,3′-dicarboxylato-κ4O,O′:O′′:O′′′] monohydrate], {[Cu(C20H12O4)(C2H7N)2]·H2O}n, (I), andcatena-poly[[aquabis(dimethylamine-κN)copper(II)]-μ-1,1′:4′,1′′-terphenyl-3,3′-dicarboxylato-κ2O3:O3′] monohydrate], {[Cu(C20H12O4)(C2H7N)2(H2O)]·H2O}n, (II), were both obtained from two different methods of preparation: one reaction was performed in the presence of 1,4-diazabicyclo[2.2.2]octane (DABCO) as a potential pillar ligand and the other was carried out in the absence of the DABCO pillar. Both reactions afforded crystals of different colours,i.e.violet plates for (I) and blue needles for (II), both of which were analysed by X-ray crystallography. The 3,3′-TPDC bridging ligands coordinate the CuIIions in asymmetric chelating modes in (I) and in monodenate binding modes in (II), forming one-dimensional chains in each case. Both coordination polymers contain two coordinated dimethylamine ligands in mutuallytranspositions, and there is an additional aqua ligand in (II). The solvent water molecules are involved in hydrogen bonds between the one-dimensional coordination polymer chains, forming a two-dimensional network in (I) and a three-dimensional network in (II).

scholarly journals Molecular Recognition in Proton-Transfer Compounds of Brucine with Achiral Substituted Salicylic Acid Analogues

2006 ◽  
Vol 59 (5) ◽  
pp. 320 ◽  
Author(s):  
Graham Smith ◽  
Urs D. Wermuth ◽  
Peter C. Healy ◽  
Jonathan M. White
Keyword(s):  
Proton Transfer ◽  
Three Dimensional ◽  
Water Molecules ◽  
Sulfosalicylic Acid ◽  
X Ray ◽  
X Ray Crystallography ◽  
Guest Species ◽  
Substituted Benzoic Acids ◽  
Proton Transfer Compounds ◽  
Hydrogen Bonded

The 1:1 proton-transfer brucinium compounds from the reaction of the alkaloid brucine with 5-nitrosalicylic acid, 3,5-dinitrosalicylic acid, and 5-sulfosalicylic acid, namely anhydrous brucinium 5-nitrosalicylate (1), brucinium 3,5-dinitrosalicylate monohydrate (2), and brucinium 5-sulfosalicylate trihydrate (3) have been prepared and their crystal structures determined by X-ray crystallography. All structures further demonstrate the selectivity of brucine for meta-substituted benzoic acids and comprise three-dimensional hydrogen-bonded framework polymers. Two of the compounds (1 and 3) have the previously described undulating brucine sheet host-substructures which incorporate interstitially hydrogen-bonded salicylate anion guest species and additionally in 3 the water molecules of solvation. The structure of 2 differs in having a three-centre brucinium–salicylate anion bidentate N+–H···O(carboxyl) hydrogen-bonding association linking the species through interstitial associations involving also the water molecules of solvation. A review of the crystallographic structural literature on strychnine and brucine is also given.

Two cadmium(II) fluorous coordination compounds tuned by different bipyridines

2017 ◽  
Vol 73 (5) ◽  
pp. 424-429 ◽  
Author(s):  
Ya-Jie Kong ◽  
Peng Li ◽  
Li-Juan Han ◽  
Lu-Tong Fan ◽  
Peng-Peng Li ◽  
...  
Keyword(s):  
Hydrogen Bond ◽  
Coordination Compounds ◽  
Linear Chain ◽  
Three Dimensional ◽  
Chain Structure ◽  
Water Molecules ◽  
Hydrogen Bond Acceptor ◽  
Small Surface ◽  
One Dimensional ◽  
Coordinated Water

Fluorine is the most electronegative element and can be used as an excellent hydrogen-bond acceptor. Fluorous coordination compounds exhibit several advantageous properties, such as enhanced high thermal and oxidative stability, low polarity, weak intermolecular interactions and a small surface tension compared to hydrocarbons. C—H...F—C interactions, although weak, play a significant role in regulating the arrangement of the organic molecules in the crystalline state and stabilizing the secondary structure. Two cadmium(II) fluorous coordination compounds formed from 2,2′-bipyridine, 4,4′-bipyridine and pentafluorobenzoate ligands, namely catena-poly[[aqua(2,2′-bipyridine-κ2 N,N′)(2,3,4,5,6-pentafluorobenzoato-κO)cadmium(II)]-μ-2,3,4,5,6-pentafluorobenzoato-κ2 O:O′], [Cd(C7F5O2)2(C10H8N2)(H2O)] n , (1), and catena-poly[[diaquabis(2,3,4,5,6-pentafluorobenzoato-κO)cadmium(II)]-μ-4,4′-bipyridine-κ2 N:N′], [Cd(C7F5O2)2(C10H8N2)(H2O)2] n , (2), have been synthesized solvothermally and structurally characterized. Compound (1) shows a one-dimensional chain structure composed of Cd—O coordination bonds and is stabilized by π–π stacking and O—H...O hydrogen-bond interactions. Compound (2) displays a one-dimensional linear chain structure formed by Cd—N coordination interactions involving the 4,4′-bipyridine ligand. Adjacent one-dimensional chains are extended into two-dimensional sheets by O—H...O hydrogen bonds between the coordinated water molecules and adjacent carboxylate groups. Moreover, the chains are further linked by C—H...F—C interactions to afford a three-dimensional network. In both structures, hydrogen bonding involving the coordinated water molecules is a primary driving force in the formation of the supramolecular structures.

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