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The complex build algorithm to set up starting structures of lanthanoid complexes with stereochemical control for molecular modeling

ABSTRACT: When handling metallic centers of higher coordination numbers, one is commonly deluded with the presumption that any assembled metal complex geometry (including a crystallographic one) is good enough as a starting structure for computational chemistry calculations; all oblivious to the fact that such a structure is nothing short of just one out of several, sometimes dozens, or even thousands of other stereoisomers. Moreover, coordination chirality, so frequently present in complexes of higher coordination numbers, is another often overlooked property, rarely recognized as such. The Complex Build algorithm advanced in this article has been designed with the purpose of generating starting structures for molecular modeling calculations with full stereochemical control, including stereoisomer complete identification and coordination chirality recognition. Besides being in the chosen correct stereochemistry, the ligands are positioned by the Complex Build algorithm in a very unobstructed and unclogged manner, so that their degrees of freedom do not hinder or even choke one another, something that would otherwise tend to lead to negative force constants after further geometry optimizations by more advanced computational model chemistries. The Complex Build algorithm has been conceived for any metallic center, but at present is targeting primarily lanthanoids whose coordination numbers range mostly from 5 to 12 and often lead to a combinatorial explosion of stereoisomers.

SUBMITTER: Munguba G

PROVIDER: S-EPMC8564551 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:We present a fragment-search based method for predicting loop conformations in protein models. A hierarchical and multidimensional database has been set up that currently classifies 105,950 loop fragments and loop flanking secondary structures. Besides the length of the loops and types of bracing secondary structures the database is organized along four internal coordinates, a distance and three types of angles characterizing the geometry of stem regions. Candidate fragments are selected from this library by matching the length, the types of bracing secondary structures of the query and satisfying the geometrical restraints of the stems and subsequently inserted in the query protein framework where their fit is assessed by the root mean square deviation (r.m.s.d.) of stem regions and by the number of rigid body clashes with the environment. In the final step remaining candidate loops are ranked by a Z-score that combines information on sequence similarity and fit of predicted and observed phi/psi main chain dihedral angle propensities. Confidence Z-score cut-offs were determined for each loop length that identify those predicted fragments that outperform a competitive ab initio method. A web server implements the method, regularly updates the fragment library and performs prediction. Predicted segments are returned, or optionally, these can be completed with side chain reconstruction and subsequently annealed in the environment of the query protein by conjugate gradient minimization. The prediction method was tested on artificially prepared search datasets where all trivial sequence similarities on the SCOP superfamily level were removed. Under these conditions it is possible to predict loops of length 4, 8 and 12 with coverage of 98, 78 and 28% with at least of 0.22, 1.38 and 2.47 A of r.m.s.d. accuracy, respectively. In a head-to-head comparison on loops extracted from freshly deposited new protein folds the current method outperformed in a approximately 5:1 ratio an earlier developed database search method.

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The complex build algorithm to set up starting structures of lanthanoid complexes with stereochemical control for molecular modeling

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