Hydrogen-bond patterns around a protein investigated by MD simulation
نویسندگان
چکیده
منابع مشابه
Hydration and hydrogen bond network of water around hydrophobic surface investigated by terahertz spectroscopy.
Water conformation around hydrophobic side chains of four amino acids (glycine, L-alanine, L-aminobutyric acid, and L-norvaline) was investigated via changes in complex dielectric constant in the terahertz (THz) region. Each of these amino acids has the same hydrophilic backbone, with successive additions of hydrophobic straight methylene groups (-CH2-) to the side chain. Changes in the degree ...
متن کاملHydrogen storage capacity of Si-decorated B80 nanocage: firstprinciples DFT calculation and MD simulation
Hydrogen storage capacity of Si-coated B80 fullerene was investigated based on density functional theory calculations within local density approximation and generalized gradient approximation. It is found that Si atom prefer to be attached above the center of pentagon with a binding energy of -5.78 eV. It is inferred that this binding is due to the charge transfer between the Si atom and B80 ca...
متن کاملRegulation of protein-ligand binding affinity by hydrogen bond pairing
Hydrogen (H)-bonds potentiate diverse cellular functions by facilitating molecular interactions. The mechanism and the extent to which H-bonds regulate molecular interactions are a largely unresolved problem in biology because the H-bonding process continuously competes with bulk water. This interference may significantly alter our understanding of molecular function, for example, in the elucid...
متن کاملHydrogen bond geometry in protein helices
Protein backbone helical structures have the same values of dihedral angles φ and ψ from unit to unit and thus, can be uniquely determined by a pair (φ,ψ). We focus our attention on two types of protein secondary structure αand 310-helices stabilized by 1-5 and 1-4 hydrogen bonding pattern respectively. Even though both αand 310-helices each represent a group of helices, various studies show th...
متن کاملPositioning hydrogen atoms by optimizing hydrogen-bond networks in protein structures.
A method is presented that positions polar hydrogen atoms in protein structures by optimizing the total hydrogen bond energy. For this goal, an empirical hydrogen bond force field was derived from small molecule crystal structures. Bifurcated hydrogen bonds are taken into account. The procedure also predicts ionization states of His, Asp, and Glu residues. During optimization, side-chain confor...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Seibutsu Butsuri
سال: 2003
ISSN: 0582-4052,1347-4219
DOI: 10.2142/biophys.43.s54_2