BACKGROUND Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces between atoms or residues during such conformational changes as observed in Molecular Dynamics (MD) simulations, we developed Time-Resolved Force Distribution Analysis (TRFDA). ...

The control of biofilm formation is a challenging goal that has not been reached yet in many aspects. One unsolved question is the role of van der Waals forces and another is the importance of mutual interactions between the adsorbing and the adsorbed biomolecules ("critical crowding"). In this study, a combined experimental and theoretical approach is presented, which fundamentally probes both...

Thermal conformational changes in human serum albumin (HSA) in present with a 10 mM phosphate buffer, at pH=7 have been investigated via circular dichroism (CD) and UV spectroscopic methods. The results indicate that temperature in a range of 25oC to 55oC could induce a reversible conformational change in the structure of HSA. The HSA phase transition corresponds to the physiological and patho...

Human alpha-Synuclein (alphaSyn) is a natively unfolded protein whose aggregation into amyloid fibrils is involved in the pathology of Parkinson disease. A full comprehension of the structure and dynamics of early intermediates leading to the aggregated states is an unsolved problem of essential importance to researchers attempting to decipher the molecular mechanisms of alphaSyn aggregation an...

background: there are two subclasses of human iga (iga1 and iga2) that differ in antigenic properties and in chemical composition. the constant domains of α1 and α2 heavy chains have >95% sequence homology though major structural differences exist in the hinge region. quantitation of iga subclass levels depends on the availability of monoclonal antibodies (mabs) specific for conserved conformat...

background: varicocele is associated with the failure of ipsilateral testicular growth and development, and the symptoms of pain and reduced fertility. the highly condensed structure of the sperm nuclear chromatin is provided by proper expression of transition nuclear protein (tnp) genes, so any dysregulational expression of these genes results in abnormal spermatogenesis and infertility. objec...

the results of mndo, am1 and pm3 semi-empirical calculations and hf/6-31g*, mp/6-31g*, mp2/6-311+g**, and b3lyp/6-311g** and qcisd/6-31g* ab initio methods for angle strain and conjugation effects in twist-boat, boat, and half-chair geometries of (z,z,z)-cycloocta-1,3,5-triene indicate that all methods, except pm3, predict wrong ordering of the conformations.

ab initio calculations at hf/6-31g* level of theory for geometry optimization and mp2/6-31g*//hf/6-31g*for total energy calculation are reported for z-cyclooctene (1). the most favorable conformation of 1 is theunsymmetric boat-chair (1-bc) geometry. potential energy profiles for two different boat-chair/boat-chairinterconversion processes were calculated. the process via a chair transition sta...