Hydrogen Bonds and Hydrophobic Interactions of Porphyrins in Porphyrin-Containing Proteins
نویسندگان
چکیده
منابع مشابه
Hydrophobic interactions and hydrogen bonds in β-sheet formation.
In this study, we investigate interactions of extended conformations of homodimeric peptides made of small (glycine or alanine) and large hydrophobic (valine or leucine) sidechains using all-atom molecular dynamics simulations to decipher driving forces for β-sheet formation. We make use of a periodic boundary condition setup in which individual peptides are infinitely long and stretched. Dimer...
متن کاملInterplay of hydrogen bonds and n→π* interactions in proteins.
Protein structures are stabilized by multiple weak interactions, including the hydrophobic effect, hydrogen bonds, electrostatic effects, and van der Waals interactions. Among these interactions, the hydrogen bond is distinct in having its origins in electron delocalization. Recently, another type of electron delocalization, the n→π* interaction between carbonyl groups, has been shown to play a...
متن کاملShort hydrogen bonds in proteins.
Short hydrogen bonds are present in many chemical and biological systems. It is well known that these short hydrogen bonds are found in the active site of enzymes and aid enzyme catalysis. This study aims to systematically characterize all short hydrogen bonds from a nonredundant dataset of protein structures. The study has revealed that short hydrogen bonds are commonly found in proteins and a...
متن کاملGeometric criteria of hydrogen bonds in proteins and identification of "bifurcated" hydrogen bonds.
Empirical criteria for identification of hydrogen bonds were analyzed to produce a set of geometrically consistent criteria. For a data set of 30 structures, application of a set of purely geometrical criteria, along with exclusion of abnormal backbone conformations, also excluded a common interaction of Ser/Thr side chains with Asp/Glu side chains ([ST]/[DE] pairs). These interactions were ter...
متن کاملWeak Interactions in Protein Folding: Hydrophobic Free Energy, van der Waals Interactions, Peptide Hydrogen Bonds, and Peptide Solvation
Hydrophobic free energy has been widely accepted as a major force driving protein folding [1, 2], although a dispute over its proper definition earlier made this issue controversial. When a hydrocarbon solute is transferred from water to a nonaqueous solvent, or a nonpolar side chain of a protein is buried in its hydrophobic core through folding, the transfer free energy is referred to as hydro...
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: The Open Structural Biology Journal
سال: 2009
ISSN: 1874-1991
DOI: 10.2174/1874199100903010034