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Minimum Energy Conformation (minimum + energy_conformation)
Selected AbstractsMacrocyclic Receptor Showing Improved PbII/ZnII and PbII/CaII SelectivitiesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 17 2010Raquel Ferreirós-Martínez Abstract Herein we report on the macrocyclic receptor N,N,-bis[(6-carboxy-2-pyridyl)methyl]-1,10-diaza-15-crown-5 (H2bp15c5) and its coordination properties towards ZnII, CdII, PbII, and CaII. The stability constants of these complexes determined by pH-potentiometric titration at 25 °C in 0.1 M KNO3 vary in the following order: PbII > CdII >> ZnII > CaII. As a result, bp15c5 presents very important PbII/ZnII and PbII/CaII selectivities. These results are in contrast to those reported for the related receptor derived from 1,7-diaza-12-crown-4, which provides very similar complex stabilities for ZnII and PbII. The X-ray crystal structure of [Cd(Hbp15c5)]+ shows heptadentate binding of the ligand to the metal ion, with two oxygen atoms of the macrocyclic unit remaining uncoordinated. The 1H NMR spectra of the complexes formed with PbII, ZnII, and CaII (D2O) show very broad peaks in the region 2,5 ppm, indicating an important degree of flexibility of the crownmoiety in these complexes. On the contrary, the 1H and 13C NMR spectra recorded for the CdII complex are well resolved and could be fully assigned. A detailed conformational investigation using theoretical calculations performed at the DFT (B3LYP) level predict a minimum energy conformation for [Cd(bp15c5)] that is very similar to that observed in the solid state. Analogous calculations performed on the [M(bp15c5)] (M = Zn or Pb) systems predict hexadentate binding of the ligand to these metal ions. In the case of the PbII complex our calculations indicate that the 6s lone pair is stereochemically active, which results in a hemidirected coordination geometry around the metal ion. The minimum energy conformations calculated for the ZnII, CdII, and PbII complexes are compatible with the experimental NMR spectra obtained in D2O solution. [source] Rotamer optimization for protein design through MAP estimation and problem-size reductionJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 12 2009Eun-Jong Hong Abstract The search for the global minimum energy conformation (GMEC) of protein side chains is an important computational challenge in protein structure prediction and design. Using rotamer models, the problem is formulated as a NP-hard optimization problem. Dead-end elimination (DEE) methods combined with systematic A* search (DEE/A*) has proven useful, but may not be strong enough as we attempt to solve protein design problems where a large number of similar rotamers is eligible and the network of interactions between residues is dense. In this work, we present an exact solution method, named BroMAP (branch-and-bound rotamer optimization using MAP estimation), for such protein design problems. The design goal of BroMAP is to be able to expand smaller search trees than conventional branch-and-bound methods while performing only a moderate amount of computation in each node, thereby reducing the total running time. To achieve that, BroMAP attempts reduction of the problem size within each node through DEE and elimination by lower bounds from approximate maximum-a-posteriori (MAP) estimation. The lower bounds are also exploited in branching and subproblem selection for fast discovery of strong upper bounds. Our computational results show that BroMAP tends to be faster than DEE/A* for large protein design cases. BroMAP also solved cases that were not solved by DEE/A* within the maximum allowed time, and did not incur significant disadvantage for cases where DEE/A* performed well. Therefore, BroMAP is particularly applicable to large protein design problems where DEE/A* struggles and can also substitute for DEE/A* in general GMEC search. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensemblesJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 10 2008Ivelin Georgiev Abstract One of the main challenges for protein redesign is the efficient evaluation of a combinatorial number of candidate structures. The modeling of protein flexibility, typically by using a rotamer library of commonly-observed low-energy side-chain conformations, further increases the complexity of the redesign problem. A dominant algorithm for protein redesign is dead-end elimination (DEE), which prunes the majority of candidate conformations by eliminating rigid rotamers that provably are not part of the global minimum energy conformation (GMEC). The identified GMEC consists of rigid rotamers (i.e., rotamers that have not been energy-minimized) and is thus referred to as the rigid-GMEC. As a postprocessing step, the conformations that survive DEE may be energy-minimized. When energy minimization is performed after pruning with DEE, the combined protein design process becomes heuristic, and is no longer provably accurate: a conformation that is pruned using rigid-rotamer energies may subsequently minimize to a lower energy than the rigid-GMEC. That is, the rigid-GMEC and the conformation with the lowest energy among all energy-minimized conformations (the minimized-GMEC) are likely to be different. While the traditional DEE algorithm succeeds in not pruning rotamers that are part of the rigid-GMEC, it makes no guarantees regarding the identification of the minimized-GMEC. In this paper we derive a novel, provable, and efficient DEE-like algorithm, called minimized-DEE (MinDEE), that guarantees that rotamers belonging to the minimized-GMEC will not be pruned, while still pruning a combinatorial number of conformations. We show that MinDEE is useful not only in identifying the minimized-GMEC, but also as a filter in an ensemble-based scoring and search algorithm for protein redesign that exploits energy-minimized conformations. We compare our results both to our previous computational predictions of protein designs and to biological activity assays of predicted protein mutants. Our provable and efficient minimized-DEE algorithm is applicable in protein redesign, protein-ligand binding prediction, and computer-aided drug design. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Study of the conformational profile of the norbornane analogues of phenylalanineJOURNAL OF PEPTIDE SCIENCE, Issue 6 2002Arnau Cordomí Abstract The conformational profile of the eight stereoisomeric 2-amino-3-phenylnorbornane-2-carboxylic acids (2-amino-3-phenylbicyclo[2.2.1]heptane-2-carboxylic acids) has been assessed by computational methods. These molecules constitute a series of four enantiomeric pairs that can be considered as rigid analogues of either L - or D -phenylalanine. The conformational space of their N -acetyl methylamide derivatives has been explored within the molecular mechanics framework, using the parm94 set of parameters of the AMBER force field. Local minimum energy conformations have been further investigated at the ab initio level by means of the Hartree-Fock and second order Moller-Plesset perturbation energy calculations using a 6,31G(d) basis set. The results of the present work suggest that the bulky norbornane structure induces two kinds of conformational constraints on the residues. On one hand, those of a steric nature directly imposed by the bicycle on the peptide backbone and, on the other hand, those that limit the orientations attainable by the phenyl ring which, in turn, reduces further the flexibility of the peptide backbone. A comparative analysis of the conformational profile of the phenylnorbornane amino acids with that of the norbornane amino acids devoid of the ,-phenyl substituent suggests that the norbornane system hampers the residue to adopt extended conformations in favour of C7-like structures. However, the bicycle itself does not impart a clear preference for any of the two possible C7 minima. It is the aromatic side chain, which is forced to adopt an almost eclipsed orientation, that breaks this symmetry introducing a marked preference for a single region of the (,, ,) conformational space in each of the phenylalanine norbornane analogues investigated. Copyright © 2002 European Peptide Society and John Wiley & Sons, Ltd. [source] Synthesis and Preferred All- syn Conformation of C3 -Symmetrical N -(Hetero)arylmethyl TriindolesCHEMISTRY - A EUROPEAN JOURNAL, Issue 28 2008Abstract A new series of C3 -symmetrical N -(hetero)arylmethyl triindoles has been synthesized in a straightforward procedure. The structure and conformation in the solid state have been determined for three derivatives (3, 4, and 6) by X-ray crystallographic analysis. In all three cases, the molecules adopt a tripodal conformation with all of the flexible arms directed towards the same side, thereby delimiting an inner cavity. Compound 6 crystallizes and forms C3 -symmetric dimeric cagelike complexes. Guest molecules of chloroform and water are confined within the resulting cavities with stabilization by different intermolecular interactions; this highlights the potential of these compounds in the construction of supramolecular systems. A computational analysis has been performed to predict the most stable conformers. As a general trend, a preference for a conformation with all branches directed to the same side has been predicted. Comparison between theoretical and experimental results indicates that the computational level selected for the present study, B3LYP/6-31G*, is able to reproduce both the minimum energy conformations and the rotation barriers about the NCH2 bond. [source] | ||||||||||