The initiation of coagulation results from the activation of factor X by an enzyme complex (Xase) composed of the trypsin-like serine proteinase, factor VIIa, bound to tissue factor (TF) on phospholipid membranes. We have investigated the basis for the protein substrate specificity of Xase using TF reconstituted into vesicles of phosphatidylcholine, phosphatidylserine, or pure phosphatidylcholi...

Delays appear in the dynamics of many systems due to non-vanishing reaction times control systems. In biochemical systems, long sequences repeated steps, especially biopolymerization processes, can be modeled by delays. However, modelling with delays is often complicated physical constraints, such as requirement that solutions representing concentrations chemical species remain positive. this w...

A new approach towards highly enantioselective halogen-bonding catalysis has been developed. In order to circumvent the intrinsic issues of halogen-bond (XB) nature and consequent unresolved limitations in asymmetric catalysis, fine-tuned halogen--halogen interactions between substrate XB-donor were designed pre-organize catalyst’s cavity boost enantiocontrol. The present strategy exploits both...

Charged, solvent-exposed residues at the entrance to the substrate binding site (gatekeeper residues) produce electrostatic dipole interactions with approaching substrates, and control their access by a novel mechanism called "electrostatic gatekeeper effect". This proof-of-concept study demonstrates that the nucleotide specificity can be engineered by altering the electrostatic properties of t...

The 3-hydroxybenzoate hydroxylase (MHBH) from Comamonas testosteroni KH122-3s is a single-component flavoprotein monooxygenase, a member of the glutathione reductase (GR) family. It catalyzes the conversion of 3-hydroxybenzoate to 3,4-dihydroxybenzoate with concomitant requirements for equimolar amounts of NADPH and molecular oxygen. The production of dihydroxy-benzenoid derivative by hydroxyla...

Resonance Raman (RR) spectroscopy is used to help define active site structural responses of nanodisc-incorporated CYP3A4 to the binding of three substrates: bromocriptine (BC), erythromycin (ERY), and testosterone (TST). We demonstrate that nanodisc-incorporated assemblies reveal much more well-defined active site RR spectroscopic responses as compared to those normally obtained with the conve...

As an approach towards unraveling the nitrogenase mechanism, we have studied binding of CO to active-site FeMo-cofactor. is not only inhibitor nitrogenase, but it also a substrate, undergoing reduction hydrocarbons (Fischer–Tropsch-type chemistry). The C?C bond forming capabilities suggest that multiple or CO-derived ligands bind active site. Herein, report crystal structure with two coordinate...

From accumulating studies of hexameric helicases, a mechano-chemical coupling mechanism has emerged which postulates that the nucleoside triphosphate (NTP) hydrolysis is sequentially coordinated together with the binding and translocation of nucleic acid substrate. Various mechano-chemical models have been proposed for different hexameric helicases with no consensus for a common mechanism. To e...

Enzyme structures determined in organic solvents show that most organic molecules cluster in the active site, delineating the binding pocket. We have developed algorithms to perform solvent mapping computationally, rather than experimentally, by placing molecular probes (small molecules or functional groups) on a protein surface, and finding the regions with the most favorable binding free ener...

A fundamental catalytic principle for protein enzymes in the use of binding interactions away from the site of chemical transformation for catalysis. We have compared the binding and reactivity of a series of oligonucleotide substrates and products of the Tetrahymena ribozyme, which catalyzes a site-specific phosphodiester cleavage reaction: CCCUCUpA+G<-->CCCUCU-OH+GpA. The results suggest that...