scholarly journals Molecular basis of flexible peptide recognition by an antibody

2020 ◽  
Vol 167 (4) ◽  
pp. 343-345
Author(s):  
Koki Makabe
Keyword(s):  
Hydrogen Bonds ◽  
High Specificity ◽  
Recognition Mechanism ◽  
Intramolecular Hydrogen Bonds ◽  
Peptide Recognition ◽  
X Ray Crystallography ◽  
Biophysical Techniques ◽  
Antibody Design ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

Abstract Antibodies can recognize various types of antigens with high specificity and affinity and peptide is one of their major targets. Understanding an antibody’s molecular recognition mechanism for peptide is important for developing clones with a higher specificity and affinity. Here, the author reviews recent progresses in flexible peptide recognition by an antibody using several biophysical techniques, including X-ray crystallography, molecular dynamics simulations and calorimetric measurements. A set of two reports highlight the importance of intramolecular hydrogen bonds that form in an unbound flexible state. Such intramolecular hydrogen bonds restrict the fluctuation of the peptide and reduce the conformational entropy, resulting in the destabilization of the unbound state and increasing the binding affinity by increasing the free energy change. These detailed analyses will aid in the antibody design in the future.

scholarly journals The Effects of the Solvents on the Macrocyclic Structures: From Rigid Pillararene to Flexible Crown Ether

2021 ◽  
Author(s):  
Shuangshuang Wang ◽  
Yanzhen Yin ◽  
Jian Gao ◽  
Xingtang Liang ◽  
Haixin Shi
Keyword(s):  
Hydrogen Bonds ◽  
Structural Design ◽  
Structural Features ◽  
Intermolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Effect Of Solvents ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen ◽  
Macrocyclic Molecules ◽  
Polarity Of Solvents

The differences in the macrocyclic structures lead to different flexibilities, and yet the effect of solvents on the conformations is not clear so far. In this work, the conformations of four representational macrocyclic molecules (pillar[5]arene, p-tert-butyl calix[6]arene, benzylic amide macrocycle and dibenzo-18-crown-6) in three solvents with distinct polarity have been studied by all-atom molecular dynamics simulations. The structural features of the macrocycles in the solvents indicate that the conformations are related to the polarity of the solvents and the formation of hydrogen bonds. For the pillar[5]arene, the benzylic amide macrocycle and the dibenzo-18-crown-6, that cannot form intramolecular hydrogen bonds, the polarity of solvents is the major contributing factor in the conformations. The formation of intramolecular hydrogen bonds, in contrast, determinates the conformations of the calix[6]arene. Furthermore, the slight fluctuations of the structures will result in tremendous change of the intramolecular hydrogen bonds of the macrocycles and the intermolecular hydrogen bonds between the macrocycles and the solvents. The current theoretical studies that serve as a basis for the macrocyclic chemistry are valuable for the efficient structural design of the macrocyclic molecules.

scholarly journals Unusual Effects of Intramolecular Hydrogen Bonds and Dipole Interaction on FTIR and NMR of Some Imines

2019 ◽  
pp. 1-6 ◽  
Author(s):  
Elham Abdalrahem Bin Selim ◽  
Mohammed Hadi Al–Douh
Keyword(s):  
Hydrogen Bonds ◽  
Chemical Shifts ◽  
Dipole Interaction ◽  
Intramolecular Hydrogen Bonds ◽  
X Ray ◽  
X Ray Crystallography ◽  
Dipole Interactions ◽  
Intramolecular Hydrogen

Unusual effects of intramolecular hydrogen bonds and dipole interactions are investigated using FTIR, NMR and X-Ray crystallography analyses of some imines. These phenomena affect both FTIR absorptions and chemical shifts.

Controlling emissive properties by intramolecular hydrogen bonds: alkyl and aryl meso‐substituted porphycenes

2021 ◽  
Author(s):  
Jacek Waluk ◽  
Arkadiusz Listkowski ◽  
Natalia Masiera ◽  
Michał Kijak ◽  
Roman Luboradzki ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

scholarly journals Crystal Structure of Escherichia coli Agmatinase: Catalytic Mechanism and Residues Relevant for Substrate Specificity

2021 ◽  
Vol 22 (9) ◽  
pp. 4769
Author(s):  
Pablo Maturana ◽  
María S. Orellana ◽  
Sixto M. Herrera ◽  
Ignacio Martínez ◽  
Maximiliano Figueroa ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Catalytic Mechanism ◽  
Conformational Dynamics ◽  
High Specificity ◽  
Arginine Decarboxylase ◽  
Space Groups ◽  
X Ray Crystallography ◽  
High Dynamics ◽  
Dynamics Simulations

Agmatine is the product of the decarboxylation of L-arginine by the enzyme arginine decarboxylase. This amine has been attributed to neurotransmitter functions, anticonvulsant, anti-neurotoxic, and antidepressant in mammals and is a potential therapeutic agent for diseases such as Alzheimer’s, Parkinson’s, and cancer. Agmatinase enzyme hydrolyze agmatine into urea and putrescine, which belong to one of the pathways producing polyamines, essential for cell proliferation. Agmatinase from Escherichia coli (EcAGM) has been widely studied and kinetically characterized, described as highly specific for agmatine. In this study, we analyze the amino acids involved in the high specificity of EcAGM, performing a series of mutations in two loops critical to the active-site entrance. Two structures in different space groups were solved by X-ray crystallography, one at low resolution (3.2 Å), including a guanidine group; and other at high resolution (1.8 Å) which presents urea and agmatine in the active site. These structures made it possible to understand the interface interactions between subunits that allow the hexameric state and postulate a catalytic mechanism according to the Mn2+ and urea/guanidine binding site. Molecular dynamics simulations evaluated the conformational dynamics of EcAGM and residues participating in non-binding interactions. Simulations showed the high dynamics of loops of the active site entrance and evidenced the relevance of Trp68, located in the adjacent subunit, to stabilize the amino group of agmatine by cation-pi interaction. These results allow to have a structural view of the best-kinetic characterized agmatinase in literature up to now.

Energies of intramolecular hydrogen bonds in some alcohols

1974 ◽  
Vol 20 (3) ◽  
pp. 414-415
Author(s):  
Ya. A. Shuster ◽  
V. A. Granzhan ◽  
P. M. Zaitsev
Keyword(s):  
Hydrogen Bonds ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen

Hydrogen bonds in derivatives of N-substituted N’-benzoyl- and N’-(2-chlorobenzoyl)thiourea

1991 ◽  
Vol 56 (4) ◽  
pp. 880-885 ◽  
Author(s):  
Oľga Hritzová ◽  
Dušan Koščík
Keyword(s):  
Hydrogen Bonds ◽  
Spectral Studies ◽  
Intramolecular Hydrogen Bonds ◽  
Tautomeric Forms ◽  
Intramolecular Hydrogen ◽  
Derivatives Of

Intramolecular hydrogen bonds of the N-H···O=C type have been detected in the derivatives of N-substituted N’-benzoyl- and N’-(2-chlorobenzoyl)thiourea on the basis of IR spectral studies. The title compounds can exist in two tautomeric forms.

Spin-spin coupling via intramolecular hydrogen bonds

1985 ◽  
Vol 25 (5) ◽  
pp. 808-810
Author(s):  
L. N. Kurkovskaya ◽  
Yu. M. Chunaev ◽  
N. M. Przhiyalgovskaya
Keyword(s):  
Hydrogen Bonds ◽  
Spin Coupling ◽  
Intramolecular Hydrogen Bonds ◽  
Intramolecular Hydrogen ◽  
Spin Spin Coupling
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