Zwitterion formation in hydrated amino acid, dipole bound anions: How many water molecules are required?

2003 ◽  
Vol 119 (20) ◽  
pp. 10696-10701 ◽  
Author(s):  
Shoujun Xu ◽  
J. Michael Nilles ◽  
Kit H. Bowen
Keyword(s):  
Amino Acid ◽  
Water Molecules ◽  
Zwitterion Formation

scholarly journals Entropy-Enthalpy Compensations Fold Proteins in Precise Ways

2021 ◽  
Vol 22 (17) ◽  
pp. 9653
Author(s):  
Jiacheng Li ◽  
Chengyu Hou ◽  
Xiaoliang Ma ◽  
Shuai Guo ◽  
Hongchi Zhang ◽  
...  
Keyword(s):  
Free Energy ◽  
Protein Folding ◽  
Amino Acid ◽  
Gibbs Free Energy ◽  
Energy Equation ◽  
Protein Structures ◽  
Water Molecules ◽  
Side Chains ◽  
Hydrophobic Collapse ◽  
Polypeptide Chains

Exploring the protein-folding problem has been a longstanding challenge in molecular biology and biophysics. Intramolecular hydrogen (H)-bonds play an extremely important role in stabilizing protein structures. To form these intramolecular H-bonds, nascent unfolded polypeptide chains need to escape from hydrogen bonding with surrounding polar water molecules under the solution conditions that require entropy-enthalpy compensations, according to the Gibbs free energy equation and the change in enthalpy. Here, by analyzing the spatial layout of the side-chains of amino acid residues in experimentally determined protein structures, we reveal a protein-folding mechanism based on the entropy-enthalpy compensations that initially driven by laterally hydrophobic collapse among the side-chains of adjacent residues in the sequences of unfolded protein chains. This hydrophobic collapse promotes the formation of the H-bonds within the polypeptide backbone structures through the entropy-enthalpy compensation mechanism, enabling secondary structures and tertiary structures to fold reproducibly following explicit physical folding codes and forces. The temperature dependence of protein folding is thus attributed to the environment dependence of the conformational Gibbs free energy equation. The folding codes and forces in the amino acid sequence that dictate the formation of β-strands and α-helices can be deciphered with great accuracy through evaluation of the hydrophobic interactions among neighboring side-chains of an unfolded polypeptide from a β-strand-like thermodynamic metastable state. The folding of protein quaternary structures is found to be guided by the entropy-enthalpy compensations in between the docking sites of protein subunits according to the Gibbs free energy equation that is verified by bioinformatics analyses of a dozen structures of dimers. Protein folding is therefore guided by multistage entropy-enthalpy compensations of the system of polypeptide chains and water molecules under the solution conditions.

scholarly journals Characterizing Hydropathy of Amino Acid Side Chain in a Protein Environment by Investigating the Structural Changes of Water Molecules Network

2021 ◽  
Vol 8 ◽  
Author(s):  
Lorenzo Di Rienzo ◽  
Mattia Miotto ◽  
Leonardo Bò ◽  
Giancarlo Ruocco ◽  
Domenico Raimondo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Amino Acid ◽  
Computational Method ◽  
Side Chain ◽  
Water Molecules ◽  
Amino Acid Side Chain ◽  
Hydrogen Bond Network ◽  
Bond Network ◽  
Protein Environment

Assessing the hydropathy properties of molecules, like proteins and chemical compounds, has a crucial role in many fields of computational biology, such as drug design, biomolecular interaction, and folding prediction. Over the past decades, many descriptors were devised to evaluate the hydrophobicity of side chains. In this field, recently we likewise have developed a computational method, based on molecular dynamics data, for the investigation of the hydrophilicity and hydrophobicity features of the 20 natural amino acids, analyzing the changes occurring in the hydrogen bond network of water molecules surrounding each given compound. The local environment of each residue is complex and depends on the chemical nature of the side chain and the location in the protein. Here, we characterize the solvation properties of each amino acid side chain in the protein environment by considering its spatial reorganization in the protein local structure, so that the computational evaluation of differences in terms of hydropathy profiles in different structural and dynamical conditions can be brought to bear. A set of atomistic molecular dynamics simulations have been used to characterize the dynamic hydrogen bond network at the interface between protein and solvent, from which we map out the local hydrophobicity and hydrophilicity of amino acid residues.

scholarly journals Bis(lysine-κ2 N,O)hexa-μ2-oxido-hexaoxidobis(1,10-phenanthroline-κ2 N,N′)dicopper(II)tetravanadium(V) tetrahydrate

IUCrData ◽  
2017 ◽  
Vol 2 (7) ◽  
Author(s):  
Ana Karen Giron-Moreno ◽  
Nancy Lara-Sánchez ◽  
Gabriela Moreno-Martínez ◽  
Cándida Pastor-Ramírez ◽  
Eduardo Sánchez-Lara ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Amino Acid ◽  
Hydrogen Bonds ◽  
Three Dimensional ◽  
Water Molecules ◽  
Formula Unit ◽  
Zwitterionic Form ◽  
Solvent Water ◽  
Dimensional Network ◽  
Intramolecular Hydrogen

The heterometallic coordination compound [Cu(Lys)(phen)]2V4O12·4H2O (Lys is the amino acid lysine, C6H14N2O2, and phen is 1,10-phenanthroline, C12H8N2) lies across an inversion centre. Two [Cu(Lys)(phen)]2+ units coordinate to the cyclo-vanadate fragment and the formula unit is completed by four solvent water molecules. The lysine ligand is in the zwitterionic form and chelates the CuII atom via the α-NH2 and α-COO− donor groups, while the ∊-NH3 + group is involved in intramolecular hydrogen bonds with the central [V4O12]4− core and with solvent water molecules. In the crystal, N—H...O and O—H...O hydrogen bonds connect the components of the structure to form a three-dimensional network. The crystal structure is further stabilized by π–π interactions involving the phen ligands. The lysine group is disordered over two sets of sites with refined occupancies of 0.534 (11) and 0.466 (11).

Amino-acid and water molecules adsorbed on water clusters in a beam

2005 ◽  
Vol 123 (7) ◽  
pp. 074301 ◽  
Author(s):  
Ramiro Moro ◽  
Roman Rabinovitch ◽  
Vitaly V. Kresin
Keyword(s):  
Amino Acid ◽  
Water Clusters ◽  
Water Molecules

scholarly journals Crystal structures and hydrogen bond analysis of five amino acid conjugates of terephthalic and benzene-1,2,3-tricarboxylic acids

CrystEngComm ◽  
2014 ◽  
Vol 16 (35) ◽  
pp. 8243-8251 ◽  
Author(s):  
Anirban Karmakar ◽  
Clive L. Oliver ◽  
Ana E. Platero-Prats ◽  
Elina Laurila ◽  
Lars Öhrström
Keyword(s):  
Hydrogen Bond ◽  
Amino Acid ◽  
Crystal Structures ◽  
Hirshfeld Surface ◽  
Water Molecules ◽  
Narrow Channels ◽  
Amino Acid Conjugates ◽  
Graph Set ◽  
Hydrogen Bond Analysis ◽  
Hydrogen Bonded

This amino acid derived (red&blue) π-stacked (green) hydrogen bonded (striped) dimer forms a pcu-net with water molecules in the narrow channels. Four related molecules are also presented and all were subjected to graph set and Hirshfeld surface analyses.

scholarly journals Influence of amino acid additives on solution behaviour of L-alanine

2018 ◽  
Vol 20 (1) ◽  
pp. 23
Author(s):  
Muhamad Fitri Othman ◽  
Nornizar Anuar ◽  
Noor Fitrah Abu Bakar ◽  
Norazah Abdul Rahman
Keyword(s):  
Amino Acid ◽  
Chemical Engineering ◽  
Gravimetric Method ◽  
Side Chain ◽  
Water Molecules ◽  
Solvent Interaction ◽  
Engineering Research ◽  
Water Solvent ◽  
Solution Behaviour ◽  
The Ideal

<p>The solubility experiment of L-alanine solution was performed in a 250ml jacketed glass crystallizer without and with amino acid additives at temperature from 15<sup>o</sup>C to 75<sup>o</sup>C by means of gravimetric method. On the whole, L-leucine additive significantly altered the solubility of L-alanine and Glycine additive caused an erratic pattern on the solubility data of L-alanine. The hydrophobic methyl side chain of L-leucine additives is believed to contribute to the formation of water clathrate in the solution which affected the interaction of L-alanine molecules in water solvent and thus modified the solubility of L-alanine. Finally, thermodynamic data analysis of L-alanine solution was extensively assessed. The negative deviation of L-alanine from the ideal solution is as a result of high solute-solvent interaction, which is due to the hydrophobicity and clathrate phenomenon of the water molecules in the solution.</p><p>Chemical Engineering Research Bulletin 20(2018) 23-29</p>

Influence of the water molecules (n = 1–6) on the interaction between Li+, Na+, K+ cations and indole molecule as tryptophan amino acid residue

2011 ◽  
Vol 23 (3) ◽  
pp. 857-865 ◽  
Author(s):  
Mehdi Shakourian-Fard ◽  
Mohammadreza Nasiri ◽  
Alireza Fattahi ◽  
Majid Vafaeezadeh
Keyword(s):  
Amino Acid ◽  
Amino Acid Residue ◽  
Water Molecules

Enhanced electron-density envelopes by extended solvent definition

1998 ◽  
Vol 54 (3) ◽  
pp. 461-466 ◽  
Author(s):  
Nick Blom ◽  
Jurgen Sygush
Keyword(s):  
Amino Acid ◽  
Electron Density ◽  
Considerable Improvement ◽  
Amino Acid Sequences ◽  
Water Molecules ◽  
E Coli ◽  
Density Maps ◽  
Weak Electron

Extended delineation of water molecules, monitored using R free values, afforded considerable improvement in quality of electron-density maps for structure determination of mammalian class I and E. coli class II aldolases. Augmented solvent definition results in an additional decrease in R free values of 3–4% and is reflected in significantly enhanced electron-density envelopes enabling tracing of amino-acid sequences through regions of otherwise discontinuous or weak electron density.

scholarly journals Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

2015 ◽  
Vol 71 (11) ◽  
pp. 2192-2202 ◽  
Author(s):  
Lada Biedermannová ◽  
Bohdan Schneider
Keyword(s):  
Amino Acid ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Solvent Accessibility ◽  
Hydration Shell ◽  
Protein Crystal ◽  
Water Molecules ◽  
Amino Acid Residues ◽  
Set Up ◽  
Dynamics Simulations

Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

Exploring the Role of Water Molecules in the Ligand Binding Domain of PDE4B and PDE4D: Virtual Screening Based Molecular Docking of Some Active Scaffolds

2019 ◽  
Vol 15 (4) ◽  
pp. 334-366
Author(s):  
Priya Singh ◽  
Mitali Mishra ◽  
Shivangi Agarwal ◽  
Samaresh Sau ◽  
Arun K. Iyer ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Amino Acid ◽  
Water Molecule ◽  
Ligand Binding ◽  
Binding Affinity ◽  
Binding Domain ◽  
Ligand Binding Domain ◽  
Water Molecules ◽  
Docking Experiment

Background: The phosphodiesterase (PDE) is a superfamily represented by four genes: PDE4A, B,C, and D which cause the hydrolysis of phosphodiester bond of cAMP to yield inactive AMP. c-AMP catalyzing enzyme is predominant in inflammatory and immunomodulatory cells. Therapy to treat Chronic Obstructive Pulmonary Disease (COPD) with the use of PDE4 inhibitors is highly envisaged. Objective: A molecular docking experiment with large dataset of diverse scaffolds has been performed on PDE4 inhibitors to analyze the role of amino acid responsible for binding and activation of the secondary transmitters. Apart from the general docking experiment, the main focus was to discover the role of water molecules present in the ligand-binding domain. Methods: All the compounds were docked in the PDE4B and PDE4D active cavity to produce the free binding energy scores and spatial disposition/orientation of chemical groups of inhibitors around the cavity. Under uniform condition, the experiments were carried out with and without water molecules in the LBD. The exhaustive study was carried out on the Autodock 4.2 software and explored the role of water molecules present in the binding domain. Results: In presence of water molecule, Roflumilast has more binding affinity (-8.48 Kcal/mol with PDE4B enzyme and -8.91 Kcal/mol with PDE4D enzyme) and forms two hydrogen bonds with Gln443 and Glu369 and amino acid with PDE4B and PDE4D enzymes respectively. While in absence of water molecule its binding affinity has decreased (-7.3 Kcal/mol with PDE4B enzyme and -5.17 Kcal/mol with PDE4D enzyme) as well as no H-bond interactions were observed. Similar observation was made with clinically tested molecules. Conclusion: In protein-ligand binding interactions, appropriate selection of water molecules facilitated the ligand binding, which eventually enhances the efficiency as well as the efficacy of ligand binding.

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