Molecular dynamics simulations of lignin peroxidase in solution.
The dynamical and structural properties of lignin peroxidase and its Trp171Ala mutant have been investigated in aqueous solution using molecular dynamics (MD) simulations. In both cases, the enzyme retained its overall backbone structure and all its noncovalent interactions in the course of the MD simulations. Very interestingly, the analysis of the MD trajectories showed the presence of large fluctuations in correspondence of the residues forming the heme access channel; these movements enlarge the opening and facilitate the access of substrates to the enzyme active site. Moreover, steered molecular dynamics docking simulations have shown that lignin peroxidase natural substrate (veratryl alcohol) can easily approach the heme edge through the access channel.
Francesca Gerini
M
M
Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Rome, Italy.
Roccatano
Danilo
D
Baciocchi
Enrico
E
Di Nola
Alfredo
A
D001592:Benzyl Alcohols / Q000737:chemistry*; D001665:Binding Sites; D002118:Calcium / Q000737:chemistry*; D003198:Computer Simulation; D003461:Crystallography / Q000379:methods*; D004789:Enzyme Activation; D004795:Enzyme Stability; D006418:Heme / Q000737:chemistry*; D008956:Models, Chemical; D008958:Models, Molecular; D009154:Mutation; D010544:Peroxidases / Q000737:chemistry*; D020075:Phanerochaete / Q000737:chemistry / Q000201:enzymology; D011485:Protein Binding; D011487:Protein Conformation; D012996:Solutions; D013329:Structure-Activity Relationship; D013379:Substrate Specificity
D001592:Benzyl Alcohols; D012996:Solutions; D006418:Heme; D010544:Peroxidases; C042858:lignin peroxidase; C042197:veratryl alcohol; D002118:Calcium