Dynamic properties of extremophilic subtilisin-like serine-proteases

Molecular motions and free-energy landscape of serine proteinase K in relation to its cold-adaptation: a comparative molecular dynamics simulation study and the underlying mechanisms

“…For an enzyme, conformational exibility is fundamental for its ability to adopt various conformations during catalytic processes, and local conformational exibility in regions involved in the catalysis is crucial for substrate degradation. 20,50,51 It is widely accepted that psychrophilic enzymes are oen characterized by enhanced exibility of the whole structure or distinct regions, which could be favor their cold-adaption. 52,53 In the present study, we performed MD simulations on the same two proteins used by Tiberti et al 20 They found that psychrophilic proteinase K did not feature an overall higher exibility with respect to the mesophilic form, but that regions near the substrate-binding cle or around calcium-binding sites showed enhanced exi-bility.…”

“…20,50,51 It is widely accepted that psychrophilic enzymes are oen characterized by enhanced exibility of the whole structure or distinct regions, which could be favor their cold-adaption. 52,53 In the present study, we performed MD simulations on the same two proteins used by Tiberti et al 20 They found that psychrophilic proteinase K did not feature an overall higher exibility with respect to the mesophilic form, but that regions near the substrate-binding cle or around calcium-binding sites showed enhanced exi-bility. Our study is in good agreement with that of Tiberti et al and, apart from the crucial functional regions studied by Tiberti et al, regions not directly involved in catalysis but close or opposite to functional sites also showed enhanced exibility.…”

“…Nevertheless, different enzymatic families can follow different strategies to cope with a low-temperature environment, 19,20 suggesting that differences in static structure and intra-molecular interactions may be not the main reason behind the cold-adaptation of psychrophilic enzymes. That is, the physicochemical basis for enzyme cold-adaptation is not known.…”

Structural investigation of the cold-adapted acylaminoacyl peptidase from Sporosarcina psychrophila by atomistic simulations and biophysical methods

“…Indeed, in the case of a pair of residues with multiple atoms involved in the interaction only one edge was considered. Interactions with persistence lower than 20% were discarded because they are poorly representative of the structural properties of the protein, as previously observed in other cases that have been studied [31,36,90,91].…”

Steered molecular dynamics simulations on the binding of the appendant structure and helix-β2 in domain-swapped human cystatin C dimer

“…We evaluated the electrostatic interactions by calculating the distances between all charged groups in the pulling region. Based upon previously published data, if the distance between two oppositely charged residues came within 0.4 nm this was defined as a salt bridge (Tiberti & Elena, 2011). Figure 7 summarizes the important salt bridges formed during the dissociation process.…”