Molecular Dynamics Simulations of the Photoactive Protein Nitrile Hydratase

Abstract

Nitrile hydratase (NHase) is an enzyme used in the industrial biotechnological production of acrylamide. The active site, which contains nonheme iron or noncorrin cobalt, is buried in the protein core at the interface of two domains, alpha and beta. Hydrogen bonds between betaArg-56 and alphaCys-114 sulfenic acid (alphaCEA114) are important to maintain the enzymatic activity. The enzyme may be inactivated by endogenous nitric oxide (NO) and activated by absorption of photons of wavelength lambda < 630 nm. To explain the photosensitivity and to propose structural determinants of catalytic activity, differences in the dynamics of light-active and dark-inactive forms of NHase were investigated using molecular dynamics (MD) modeling. To this end, a new set of force field parameters for nonstandard NHase active sites have been developed. The dynamics of the photodissociated NO ligand in the enzyme channel was analyzed using the locally enhanced sampling method, as implemented in the MOIL MD package. A series of 1 ns trajectories of NHases shows that the protonation state of the active site affects the dynamics of the catalytic water and NO ligand close to the metal center. MD simulations support the catalytic mechanism in which a water molecule bound to the metal ion directly attacks the nitrile carbon.

Enzymatic mechanism and biochemistry for cyanide degradation: A review

“…The mechanism by which the cobalt is transported to nitrile hydratase without causing toxicity is unclear, although a cobalt permease has been identified, which transports cobalt across the cell membrane [50].Metabolic pathway In some bacteria and fungi, nitrile hydratase and amidase are present together and are responsible for the sequential metabolism of nitriles. These microbes are capable of utilizing aliphatic nitriles as the sole source of nitrogen and carbon.…”

Catalytic Mechanism of Nitrile Hydratase Proposed by Time-resolved X-ray Crystallography Using a Novel Substrate, tert-Butylisonitrile

“…Kovacs and co-workers (14) studied the ligand exchange reaction in the low spin Co 3ϩ -containing NHase model complexes and concluded that the trans-thiolate sulfur played an important role in promoting the ligand exchange at the sixth site. Later, by using a sulfenate-ligated iron complex, they showed that protonation/deprotonation states of the sulfenate oxygen were modulated by the unmodified Cys thiolate ligand (15) (19,20) as well as molecular dynamics simulations (21), have been applied to the mechanisms described above. However, the detailed mechanism remains unclear because of a lack of direct information on the reaction intermediates.…”

Fibronectin Module FNIII9 Adsorption at Contrasting Solid Model Surfaces Studied by Atomistic Molecular Dynamics

“…We note that there are no cysteine and only one methionine (Met48); these residues can provide sulfur for protein -gold interactions 9 . Despite its limitations, namely the simulation time (usually tens to hundreds of nanoseconds are simulated with commonly available computational resources), the system size (the larger molecule, the shorter accessible simulation time) and the forcefield parameterization (the potentials used to describe both bonding and nonbonding interactions of the system), MD simulation has proven its utility to study peptide and protein dynamics in general [10][11][12] and its adsorption in particular. [13][14][15][16][17][18][19][20][21][22][23][24][25][26] MD can provide a unique insight into the initial adsorption processes.…”