Rapid and selective ion transport is essential for the generation and regulation of electrical signaling pathways in living organisms. Here, we use molecular dynamics (MD) simulations with an applied membrane potential to investigate the ion flux of bacterial sodium channel NaVMs. 5.9 µs simulations with 500 mM NaCl suggest different mechanisms for inward and outward flux. The predicted inward ...

The autosomal dominantly inherited disease AIP (acute intermittent porphyria) is caused by mutations in HMBS [hydroxymethylbilane synthase; also known as PBG (porphobilinogen) deaminase], the third enzyme in the haem biosynthesis pathway. Enzyme-intermediates with increasing number of PBG molecules are formed during the catalysis of HMBS. In this work, we studied the two uncharacterized mutants...

Many enzymes mold their structures to enclose substrates in their active sites such that conformational remodeling may be required during each catalytic cycle. In adenylate kinase (AK), this involves a large-amplitude rearrangement of the enzyme's lid domain. Using our method of high-resolution single-molecule FRET, we directly followed AK's domain movements on its catalytic time scale. To quan...

Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the conformational fluctuations of proteins in their folded state. This so-called Gaussian network model (GNM) is applied here to the interpretation of experimental hydrogen exchange (HX) behavior of proteins in their native state or under weakly den...

Since the proposal of 'in-line attack' conformation as a possibly important intermediate in RNA cleavage, its structure has been captured in various protein and RNA enzymes; these structures strengthen the belief that this conformation plays an essential role in the catalysis of RNA cleavage. As generally discussed, this intermediate structure can be involved in energy barrier reduction in two ...

Antibody arrays were developed to probe a monoclonal antibody's three-dimensional structure (3-D structure). Peptides with overlapping regions were designed to cover the whole mAb light chain and heavy chain, respectively, and used to generate polyclonal antibodies after the conjugation of the peptides to a carrier protein, KLH. It was shown that good peptide specificity was achieved from the a...

The hybrid density functional theory (B3LYP) and ab initio molecular orbital (HF) based methods and Natural Bond Orbital (NBO) interpretation were used to analyze the conformational behaviors of 2,5,5-trimethyl-1,3,2-dioxaphosphinane 2-selenide (compound 1), 2,5,5-trimethyl-1,3,2-dithiaphosphinane 2-selenide (compound 2) and 2,5,5-trimethyl-1,3,2-diselena phosp...

Conformational heterogeneity leads to different excited state relaxation pathways in flexibly-linked DPP-dimers.

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...