Bifurcated Hydrogen Bonds Stabilize Fibrils of Poly(l-glutamic) Acid

2010 ◽  
Vol 114 (24) ◽  
pp. 8278-8283 ◽  
Author(s):  
Aleksandra Fulara ◽  
Wojciech Dzwolak
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid

WHICH IS THE PROTON-SHUTTLE IN ISOXANTHOPTERIN DEAMINASE? QM/MM MD UNDERSTANDING

2013 ◽  
Vol 12 (08) ◽  
pp. 1341002 ◽  
Author(s):  
XIN ZHANG ◽  
MING LEI
Keyword(s):  
Crystal Structure ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Proton Transfer ◽  
Glutamic Acid ◽  
Active Site ◽  
Nucleophilic Attack ◽  
Zinc Ions ◽  
Initial Model ◽  
Dynamics Simulations

The deamination process of isoxanthopterin catalyzed by isoxanthopterin deaminase was determined using the combined QM(PM3)/MM molecular dynamics simulations. In this paper, the updated PM3 parameters were employed for zinc ions and the initial model was built up based on the crystal structure. Proton transfer and following steps have been investigated in two paths: Asp336 and His285 serve as the proton shuttle, respectively. Our simulations showed that His285 is more effective than Aap336 in proton transfer for deamination of isoxanthopterin. As hydrogen bonds between the substrate and surrounding residues play a key role in nucleophilic attack, we suggested mutating Thr195 to glutamic acid, which could enhance the hydrogen bonds and help isoxanthopterin get close to the active site. The simulations which change the substrate to pterin 6-carboxylate also performed for comparison. Our results provide reference for understanding of the mechanism of deaminase and for enhancing the deamination rate of isoxanthopterin deaminase.

Thermal-induced transformation of glutamic acid to pyroglutamic acid and self-cocrystallization: a charge–density analysis

2022 ◽  
Vol 78 (2) ◽  
Author(s):  
Sehrish Akram ◽  
Arshad Mehmood ◽  
Sajida Noureen ◽  
Maqsood Ahmed
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Single Crystal ◽  
Diffraction Data ◽  
Density Functional ◽  
Quantitative Estimation ◽  
Topological Analysis ◽  
Pyroglutamic Acid ◽  
X Ray Diffraction ◽  
X Ray

Thermal-induced transformation of glutamic acid to pyroglutamic acid is well known. However, confusion remains over the exact temperature at which this happens. Moreover, no diffraction data are available to support the transition. In this article, we make a systematic investigation involving thermal analysis, hot-stage microscopy and single-crystal X-ray diffraction to study a one-pot thermal transition of glutamic acid to pyroglutamic acid and subsequent self-cocrystallization between the product (hydrated pyroglutamic acid) and the unreacted precursor (glutamic acid). The melt upon cooling gave a robust cocrystal, namely, glutamic acid–pyroglutamic acid–water (1/1/1), C5H7NO3·C5H9NO4·H2O, whose structure has been elucidated from single-crystal X-ray diffraction data collected at room temperature. A three-dimensional network of strong hydrogen bonds has been found. A Hirshfeld surface analysis was carried out to make a quantitative estimation of the intermolecular interactions. In order to gain insight into the strength and stability of the cocrystal, the transferability principle was utilized to make a topological analysis and to study the electron-density-derived properties. The transferred model has been found to be superior to the classical independent atom model (IAM). The experimental results have been compared with results from a multipolar refinement carried out using theoretical structure factors generated from density functional theory (DFT) calculations. Very strong classical hydrogen bonds drive the cocrystallization and lend stability to the resulting cocrystal. Important conclusions have been drawn about this transition.

Side chain-backbone hydrogen bonds in peptides containing glutamic acid residues

Biopolymers ◽  
1979 ◽  
Vol 18 (5) ◽  
pp. 1293-1296 ◽  
Author(s):  
Roger Mayer ◽  
G�rard Lancelot ◽  
G�rard Spach
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Side Chain

scholarly journals Probing the conformation of a conserved glutamic acid within the Cl− pathway of a CLC H+/Cl− exchanger

2017 ◽  
Vol 149 (4) ◽  
pp. 523-529 ◽  
Author(s):  
Malvin Vien ◽  
Daniel Basilio ◽  
Lilia Leisle ◽  
Alessio Accardi
Keyword(s):  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Transport Proteins ◽  
Side Chain ◽  
Ion Binding ◽  
Computational Studies ◽  
Transport Models ◽  
Ions Transport ◽  
Selective Transport ◽  
Transport Cycle

The CLC proteins form a broad family of anion-selective transport proteins that includes both channels and exchangers. Despite extensive structural, functional, and computational studies, the transport mechanism of the CLC exchangers remains poorly understood. Several transport models have been proposed but have failed to capture all the key features of these transporters. Multiple CLC crystal structures have suggested that a conserved glutamic acid, Gluex, can adopt three conformations and that the interconversion of its side chain between these states underlies H+/Cl− exchange. One of these states, in which Gluex occupies the central binding site (Scen) while Cl− ions fill the internal and external sites (Sint and Sext), has only been observed in one homologue, the eukaryotic cmCLC. The existence of such a state in other CLCs has not been demonstrated. In this study, we find that during transport, the prototypical prokaryotic CLC exchanger, CLC-ec1, adopts a conformation with functional characteristics that match those predicted for a cmCLC-like state, with Gluex trapped in Scen between two Cl− ions. Transport by CLC-ec1 is reduced when [Cl−] is symmetrically increased on both sides of the membrane and mutations that disrupt the hydrogen bonds stabilizing Gluex in Scen destabilize this trapped state. Furthermore, inhibition of transport by high [Cl−] is abolished in the E148A mutant, in which the Gluex side chain is removed. Collectively, our results suggest that, during the CLC transport cycle, Gluex can occupy Scen as well as the Sext position in which it has been captured crystallographically and that hydrogen bonds with the side chains of residues that coordinate ion binding to Scen play a role in determining the equilibrium between these two conformations.

scholarly journals Synthesis of nonracemic hydroxyglutamic acids

2019 ◽  
Vol 15 ◽  
pp. 236-255
Author(s):  
Dorota G Piotrowska ◽  
Iwona E Głowacka ◽  
Andrzej E Wróblewski ◽  
Liwia Lubowiecka
Keyword(s):  
Natural Products ◽  
Carbon Atom ◽  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Functional Groups ◽  
Review Article ◽  
Cellular Processes ◽  
Structural Analogues ◽  
Derivatives Of ◽  
Additional Hydrogen

Glutamic acid is involved in several cellular processes though its role as the neurotransmitter is best recognized. For detailed studies of interactions with receptors a number of structural analogues of glutamic acid are required to map their active sides. This review article summarizes syntheses of nonracemic hydroxyglutamic acid analogues equipped with functional groups capable for the formation of additional hydrogen bonds, both as donors and acceptors. The majority of synthetic strategies starts from natural products and relies on application of chirons having the required configuration at the carbon atom bonded to nitrogen (e.g., serine, glutamic and pyroglutamic acids, proline and 4-hydroxyproline). Since various hydroxyglutamic acids were identified as components of complex natural products, syntheses of orthogonally protected derivatives of hydroxyglutamic acids are also covered.

Aspartic Acid-Aspartate and Glutamic Acid-Glutamate Hydrogen Bonds Having Great Proton Polarizability — IR Investigations

1981 ◽  
Vol 36 (11-12) ◽  
pp. 961-963 ◽  
Author(s):  
Pushti Prakash Rastogi ◽  
Georg Zundel
Keyword(s):  
Ir Spectroscopy ◽  
Hydrogen Bonds ◽  
Glutamic Acid ◽  
Positive Charge ◽  
Carboxylate Group ◽  
Acid Anion ◽  
Proton Potential ◽  
Protein Molecules ◽  
Stretching Vibration ◽  
Anion Complexes

Abstract α-Amino and α-carboxylate group protected aspartate (Z-asp-OMe) and glutamate (Z-glu-OBZl) solutions in CH2Cl2 are studied as function of the addition of the respective salts by IR spectroscopy. The antisymmetrical stretching vibration of the -CO2c- groups shifts to the position where v C = O of the acid groups is observed, indicating that both anions in the acid-anion complexes are strongly influenced by the proton. With the formation of these complexes a continuum arises preferentially in the region 1600-900 cm-1 demonstrating that the OH · · · O- ⇌ -O · · · HO bonds formed show great proton polarizability. These hydrogen bonds are short and the proton potential is probably a broad flat well. The degree of the formation of these hydrogen bonds is determined. Finally, it is discussed that positive charge can easily be translocated via such hydrogen bonds in protein molecules.

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