The surface parameter of nanoparticles such as hydrophobicity and a hydrophilicity on protein structure and function is very important. In this study, conformational changes of glucose oxidase (GOx) in the mercaptopurine: GNPs and 11-mercaptoundecanoic acid: GNPs as a hydrophobic and a hydrophilic GNPs surface was investigated by various spectroscopic techniques, including: UV-Vis absorption, f...

The quantum-chemical calculations on the conformational properties of 2-flouro-2-oxo- 1,3,2-dioxaphosphorinane (1), 2-choloro-2-oxo-1,3,2-dioxaphosphorinane (2) and 2-bromo- 2-oxo-1,3,2-dioxaphosphorinane (3) have been investigated by means of ab initio molecular orbital (HF/6-311+G**) and hybrid density functional theory (B3LYP/6-311+G**) based methods and Natural Bond Orbital (NBO) interpreta...

Understanding the conformational propensities of proteins is key to solving many problems in structural biology and biophysics. The co-variation of pairs of mutations contained in multiple sequence alignments of protein families can be used to build a Potts Hamiltonian model of the sequence patterns which accurately predicts structural contacts. This observation paves the way to develop deeper ...

When analyzing single-molecule data, a low-dimensional set of system observables typically serves as the observational data. We calibrate stochastic dynamical models from time series that record such observables. Numerical techniques for quantifying noise from multiple time scales in a single trajectory, including experimental instrument and inherent thermal noise, are demonstrated. The techniq...

The manifold array of saccharide linkages leads to a great variety polysaccharide architectures, comprising three conformations in aqueous solution: compact sphere, random coil, and rigid rod. This conformational variation limits the suitability commonly applied molecular weight cut-off (MWCO) as selection criteria for ultrafiltration membranes, it is based on globular marker proteins with narr...

In this work, quaternary conformational studies of peanut agglutinin (PNA) have been carried out using small-angle X-ray scattering (SAXS). PNA was submitted to three different conditions: pH variation (2.5, 4.0, 7.4 and 9.0), guanidine hydrochloride presence (0.5-2M) at each pH value, and temperature ranging from 25 to 60°C. All experiments were performed in the absence and presence of T-antig...

Amino acids display significant variation in propensity for the alpha R-helical, beta-sheet, and other main chain conformational states in proteins and peptides. The physical reason for these preferences remains controversial. Conformational entropy, steric factors, and the hydrophobic effect have all been advanced as the dominant underlying cause. In this work, we explore the role of a fourth ...

MOTIVATION Alternative structural models determined experimentally are available for an increasing number of proteins. Structural and functional studies of these proteins need to take these models into consideration as they can present considerable structural differences. The characterization of the structural differences and similarities between these models is a fundamental task in structural...

nbo analysis, hybrid density functional theory (b3lyp/6-311+g**) and ab initio molecular orbital (hf/6-311+g**) based methods were used to study the anomeric effects (ae), electrostatic interactions, dipole-dipole interactions and steric repulsion effects on the conformational properties of 2-methoxy- (1), 2-methylthio- (2), 2-methylseleno- (3), 2-fluoro- (4), 2-chloro- (5) and 2-bromocyclohexa...

Conformational properties of a 12-residue tryptophan zipper (trpzip) beta-hairpin peptide (AWAWENGKWAWK-NH(2), a modification of the original trpzip2 sequence) are analyzed under equilibrium conditions using ECD and IR spectra of a series of variants, singly and doubly C(1)-labeled with (13)C on the amide CO. The characteristic features of the (13)CO component of the amide I' IR band and their ...