By Tatyana Karabencheva-Christova
Combined Quantum Mechanical and Molecular Mechanical Modelling of Biomolecular Interactions keeps the culture of the Advances in Protein Chemistry and Structural Biology sequence has been the fundamental source for protein chemists.
Each quantity brings forth new information regarding protocols and research of proteins, with every one thematically prepared quantity visitor edited through major specialists in a large variety of protein-related topics.
- Describes advances in software of strong suggestions within the biosciences
- Provides state of the art advancements in protein chemistry and structural biology
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Additional info for Combined quantum mechanical and molecular mechanical modelling of biomolecular interactions
RECENT DEVELOPMENTS One of the major challenges of in silico simulations on complex biological systems is to treat several chemically active zones concurrently 24 Juan Torras et al. because their distinct evolution is linked critically to the global system behavior. Very recently, the capability for handling such multiple, disjoint QM zones in QM/MM-MD simulations has been developed within the PUPIL framework (Torras, 2015). , the ferritin cage (see Fig. 3), ubiquinone oxidoreductase and Laccase, among others.
In this work, we have applied this strategy to study two mycobacterial zinc hydrolases. Mycobacterium tuberculosis infections are still a worldwide problem and thus characterization and validation of new drug targets is an intense field of research. Among possible drug targets, recently two essential zinc hydrolases, MshB (Rv1170) and MA-amidase (Rv3717), have been proposed and structurally characterized. Although possible mechanisms have been proposed by analogy to the widely studied human Zn hydrolases, several key issues, particularly those related to Zn coordination sphere and its role in catalysis, remained unanswered.
Substrate was built independently and docked by superimposition in place, using as a constraint that scissile bond carbonyl oxygen matches position of the removed water. , 2013), PDBid 4M6G, which is bound to the reaction product L-alanineiso-D-glutamine and one additional water molecule near the active site. Calculation of Enzyme Reaction FEPs Using HyDRA 43 The substrate was placed in the active site using as a template the structural alignment between MA-amidase Rv3717 and E. coli AmiD PDBid 3D2Y which was crystallized with the bound substrate anhydro-N-acetylmuramic acid-L-Ala-D-gamma-Glu-L-Lys, performing a biased docking.