title: The planar conformation of a strained proline ring: a QM/MM study.
abstract: QM and QM/MM energy calculations have been carried out on an atomic resolution structure of liganded triosephosphate isomerase (TIM) that has an active site proline (Pro168) in a planar conformation. The origin of the planarity of this proline has been identified. Steric interactions between the atoms of the proline ring and a tyrosine ring (Tyr166) on one side of the proline prevent the ring from adopting the up pucker (chi1 is approximately -30 degrees), while the side chain of a nearby alanine (Ala171) forbids the down pucker (chi1 is approximately +30 degrees). To obtain a proline conformation that is in agreement with the experimentally observed planar state, a quantum system of sufficient size is required and should at least include the nearby side chains of Tyr166, Ala171, and Glu129 to provide enough stabilization. It is argued that the current force fields for structure optimization do not describe strained protein fragments correctly. The proline is part of a catalytic loop that closes upon ligand binding. Comparison of the proline conformation in different TIM X-ray structures, indicates that in the closed conformation of TIM the proline is planar or nearly planar, while in the open conformation it is down puckered. This suggests that the planarity possibly plays a role in the overall catalytic cycle of TIM, presumable acting as a reservoir of energy that becomes available upon loop opening.
authors.affiliation: The Biocenter and the Department of Biochemistry, University of Oulu, FIN-90014 University of Oulu, Finland.
authors.forename: Serena
authors.initials: S
authors.lastname: Donnini
authors.forename: Gerrit
authors.initials: G
authors.lastname: Groenhof
authors.forename: Rik K
authors.initials: RK
authors.lastname: Wierenga
authors.forename: André H
authors.initials: AH
authors.lastname: Juffer
mesh_terms: D000409:Alanine / Q000737:chemistry; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods; D018360:Crystallography, X-Ray / Q000379:methods; D018698:Glutamic Acid / Q000737:chemistry; D008958:Models, Molecular; D015394:Molecular Structure; D011392:Proline / Q000737:chemistry*; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D013816:Thermodynamics; D014305:Triose-Phosphate Isomerase / Q000737:chemistry*; D014443:Tyrosine / Q000737:chemistry
chemical_list: D018698:Glutamic Acid; D014443:Tyrosine; D011392:Proline; D014305:Triose-Phosphate Isomerase; D000409:Alanine