title: Molecular dynamics simulations of lignin peroxidase in solution.
abstract: 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.
authors.affiliation: Dipartimento di Chimica, Università degli Studi di Roma La Sapienza, Rome, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Francesca Gerini
authors.forename: Danilo
authors.initials: D
authors.lastname: Roccatano
authors.forename: Enrico
authors.initials: E
authors.lastname: Baciocchi
authors.forename: Alfredo
authors.initials: A
authors.lastname: Di Nola
mesh_terms: 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
chemical_list: D001592:Benzyl Alcohols; D012996:Solutions; D006418:Heme; D010544:Peroxidases; C042858:lignin peroxidase; C042197:veratryl alcohol; D002118:Calcium