title: Exploring the energy landscapes of flexible molecular loops using higher-dimensional continuation.
abstract: The conformational space of a flexible molecular loop includes the set of conformations fulfilling the geometric loop-closure constraints and its energy landscape can be seen as a scalar field defined on this implicit set. Higher-dimensional continuation tools, recently developed in dynamical systems and also applied to robotics, provide efficient algorithms to trace out implicitly defined sets. This article describes these tools and applies them to obtain full descriptions of the energy landscapes of short molecular loops that, otherwise, can only be partially explored, mainly via sampling. Moreover, to deal with larger loops, this article exploits the higher-dimensional continuation tools to find local minima and minimum energy transition paths between them, without deviating from the loop-closure constraints. The proposed techniques are applied to previously studied molecules revealing the intricate structure of their energy landscapes.
authors.affiliation: Institut de Robótica i Informática Industrial, UPC-CSIC, Llorens Artigas 4-6, 08028 Barcelona, Spain. porta@iri.upc.edu
authors.forename: Josep M
authors.initials: JM
authors.lastname: Porta
authors.forename: Léonard
authors.initials: L
authors.lastname: Jaillet
mesh_terms: D000465:Algorithms; D018797:Cell Cycle Proteins / Q000737:chemistry*; D034242:Cyclooctanes / Q000737:chemistry*; D004926:Escherichia coli / Q000737:chemistry*; D007780:Lacticaseibacillus casei / Q000737:chemistry / Q000201:enzymology*; D008780:Methyltransferases / Q000737:chemistry*; D008958:Models, Molecular; D008968:Molecular Conformation; D011487:Protein Conformation; D013762:Tetrahydrofolate Dehydrogenase / Q000737:chemistry*; D013816:Thermodynamics
chemical_list: D018797:Cell Cycle Proteins; D034242:Cyclooctanes; D013762:Tetrahydrofolate Dehydrogenase; D008780:Methyltransferases; C102247:rlmE protein, E coli; C474479:cyclooctane