ATP is required for nucleation of actin filament branches by Arp2/3 complex, but the influence of ATP binding and hydrolysis are poorly understood. We determined crystal structures of bovine Arp2/3 complex cocrystallized with various bound adenine nucleotides and cations. Nucleotide binding favors closure of the nucleotide-binding cleft of Arp3, but no large-scale conformational changes in the ...

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...

Developing drug-like molecules to inhibit the interactions formed by disordered proteins is desirable due to the high correlation of disorder with protein implicated in disease, but is challenging due in part to the lack of atomistically resolved and resolvable structures from conformationally dynamic systems. Ion mobility mass spectrometry (IM-MS) is well-positioned to assess protein ligand in...

mndo semi-empirical scf mo calculations are used to study the pyramidal nitrogen atom inversion and configurational equilibria in the title compounds.

In the past, enzymatic activity has always been expected to be dependent on overall protein rigidity, necessary for substrate recognition and optimal orientation. However, increasing evidence is now accumulating, revealing that some proteins characterized by intrinsic disorder are actually able to perform catalysis. Among them, the only known natural intrinsically disordered enzyme is UreG, a G...

The thermal denaturation (melting) of DNA molecules is a thermodynamic and conformational order-disorder transition from a double-stranded to a single-stranded state. Modeling DNA melting at the atomistic level is severely hampered due to the time and length scales of this transition. We propose a coarse-grained model where DNA strands are represented as oligomer chains of N beads using the sin...

BACKGROUND Neutralization sensitivity of HIV-1 virus to antibodies and anti-sera varies greatly between the isolates. Significant role of V1/V2 domain as a global neutralization sensitivity regulator has been suggested. Recent X-ray structures revealed presence of well-defined tertiary structure within this domain but also demonstrated partial disorder and conformational heterogeneity. METHOD...

In contrast to the notion established for many years that protein function depends on rigid 3D structures, nowadays there is important evidence suggesting that non-structured segments of proteins play important roles in protein function. Therefore, disorder-to-order dynamic conformational transitions have been proposed as an attractive mechanism involved in protein-protein recognition. Our labo...