Home About us Contact
|
Home About us Contact | ||
|
|
||
Energetic Contribution (energetic + contribution)
Selected AbstractsHeat capacity changes associated with nucleic acid foldingBIOPOLYMERS, Issue 1 2006Peter J. Mikulecky Abstract Whereas heat capacity changes (,CPs) associated with folding transitions are commonplace in the literature of protein folding, they have long been considered a minor energetic contributor in nucleic acid folding. Recent advances in the understanding of nucleic acid folding and improved technology for measuring the energetics of folding transitions have allowed a greater experimental window for measuring these effects. We present in this review a survey of current literature that confronts the issue of ,CPs associated with nucleic acid folding transitions. This work helps to gather the molecular insights that can be gleaned from analysis of ,CPs and points toward the challenges that will need to be overcome if the energetic contribution of ,CP terms are to be put to use in improving free energy calculations for nucleic acid structure prediction. © 2006 Wiley Periodicals, Inc. Biopolymers 82: 38,58, 2006 This article was originally published online as an accepted preprint. The "Published Online" date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com [source] Covalent Linkage Mediates Communication between ACP and TE Domains in Modular Polyketide SynthasesCHEMBIOCHEM, Issue 6 2008Lucky Tran Abstract Polyketide natural products such as erythromycin A and epothilone are assembled on multienzyme polyketide synthases (PKSs), which consist of modular sets of protein domains. Within these type I systems, the fidelity of biosynthesis depends on the programmed interaction among the multiple domains within each module, centered around the acyl carrier protein (ACP). A detailed understanding of interdomain communication will therefore be vital for attempts to reprogram these pathways by genetic engineering. We report here that the interaction between a representative ACP domain and its downstream thioesterase (TE) is mediated largely by covalent tethering through a short "linker" region, with only a minor energetic contribution from protein,protein molecular recognition. This finding helps explain in part the empirical observation that TE domains can function out of their normal context in engineered assembly lines, and supports the view that overall PKS architecture may dictate at least a subset of interdomain interactions. [source] Dissection of Conformationally Restricted Inhibitors Binding to a ,-GlucosidaseCHEMBIOCHEM, Issue 5 2006Tracey M. Gloster Dr. Glycosidase inhibition, important in the quest for highly potent and specific drugs, can be achieved by mimicking the oxocarbenium ion-like transition-state species that form during the catalytic mechanism. Castanospermine (left) and calystegine B2 (right) are potent inhibitors that are conformationally restricted by the inclusion of ethylene linkers. Their binding to a ,-glucosidase from Thermotoga maritima has been studied by structural, kinetic and thermodynamic methods. Although both compounds inhibit with a similar potency, castanospermine derives the majority of it energetic contribution from enthalpy whereas calystegine B2 binding is more entropically driven. [source] Progress in the Understanding of Drug,Receptor Interactions, Part,2: Experimental and Theoretical Electrostatic Moments and Interaction Energies of an Angiotensin II Receptor Antagonist (C30H30N6O3S)CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2007Raffaella Soave Dr. Abstract A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug,receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17,K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of S,,,O and S,,,N intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NH,,,N hydrogen bond with an energy of about 50,kJ,mol,1. Key pharmacophoric features responsible for attractive electrostatic interactions include CH,,,X hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions. [source] Thermodynamic and kinetic analyses for understanding sequence-specific DNA recognitionGENES TO CELLS, Issue 5 2000Masayuki Oda Thermodynamic and kinetic analyses of biomolecular interactions reveal details of the energetic and dynamic features of molecular recognition processes, and complement structural analyses of the free and complexed conformations. The recent improvements in both isothermal titration calorimetry and surface plasmon resonance sensoring provide powerful tools for analysing biomolecular interactions in thermodynamic and kinetic approaches. The thermodynamic and kinetic parameters obtained for binding between protein and DNA indicate the mechanism of specific DNA recognition, in the high-resolution structures of the protein,DNA complexes. The effects of temperature and ionic strength reflect the conformational changes of the protein and DNA molecules upon complex formation, including important contributions of water and solutes. When combined with mutational studies, the interactions can be reduced to several energetic contributions from individual contacts. These studies should be useful to determine general features of protein functions in genetic regulation. [source] An efficient algorithm for multistate protein design based on FASTERJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 5 2010Benjamin D. Allen Abstract Most of the methods that have been developed for computational protein design involve the selection of side-chain conformations in the context of a single, fixed main-chain structure. In contrast, multistate design (MSD) methods allow sequence selection to be driven by the energetic contributions of multiple structural or chemical states simultaneously. This methodology is expected to be useful when the design target is an ensemble of related states rather than a single structure, or when a protein sequence must assume several distinct conformations to function. MSD can also be used with explicit negative design to suggest sequences with altered structural, binding, or catalytic specificity. We report implementation details of an efficient multistate design optimization algorithm based on FASTER (MSD-FASTER). We subjected the algorithm to a battery of computational tests and found it to be generally applicable to various multistate design problems; designs with a large number of states and many designed positions are completely feasible. A direct comparison of MSD-FASTER and multistate design Monte Carlo indicated that MSD-FASTER discovers low-energy sequences much more consistently. MSD-FASTER likely performs better because amino acid substitutions are chosen on an energetic basis rather than randomly, and because multiple substitutions are applied together. Through its greater efficiency, MSD-FASTER should allow protein designers to test experimentally better-scoring sequences, and thus accelerate progress in the development of improved scoring functions and models for computational protein design. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Pooled energy budget and human life historyAMERICAN JOURNAL OF HUMAN BIOLOGY, Issue 4 2009Meredith W. Reiches Human life history contains a series of paradoxes not easily explained by classical life history theory. Although overall reproductive output is higher than in related primates, juvenile growth is slower and age-specific reproductive rates decline faster with age. A simple energetic model would predict that growth and reproductive rates should be positively correlated and that reproductive effort should not decelerate with age. The pattern of negative correlations in humans suggest the presence of trade-offs among peak reproductive rate, childhood growth, and reproductive rate at older ages. To address this puzzle, we propose a synthesis of reproductive ecology and behavioral ecology focused on intra- and inter-somatic energy transfers. This integration includes three concepts: the mother as final common pathway through which energy must pass to result in offspring; a distinction between direct and indirect reproductive effort, proposing the latter as a novel net energy allocation category relative to growth and direct reproductive effort; and a pooled energy budget representing the energetic contributions and withdrawals of all members of a breeding community. Individuals at all reproductive life stages are considered in light of their contributions to the pooled energy budget. Am. J. Hum. Biol., 2009. © 2009 Wiley-Liss, Inc. [source] | |||||||||||||