Toward a computed peptide structure database: The role of a universal atomic numbering system of amino acids in peptides and internal hierarchy of database

Abstract

ABSTRACT:With the construction and implementation of a logical and standardized numbering of atomic nuclei, to define mono-, di-, and oligo-peptide systems, automation of input file generation and data extraction could greatly improve the efficiency of the search for the structural energy minima on the potential energy hypersurface of these systems. The internal hierarchy of the database covering constitutional structures, protective groups, levels of theory, and basis sets used, as well as the variety of possible conformations, is also discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem 90: 933-968, 2002 Key words: peptide computations; atomic numbering; protein folding; internal coordinates; database internal hierarchy; ab initio DedicationT his article is written in the "teaching spirit" of our immortal teacher Professor P. O. Löwdin. We hope that our article and the methodology and ideals within will improve the understanding of young researchers in the whole field of molecular science, from physics and mathematics through chemistry and biology, all the way to medicine and even computational sciences, specifically for those who wish to enter the field of study comprising peptide and protein folding. In this spirit, we wish to dedicate this article to the legacy and living memory of Professor P. O. Löwdin. PreambleWe are now in a new age where we are able to produce vast amounts of data but do not capitalize on their value. We cannot thoroughly analyze all of the data, due to limitations in extraction of relevant variables and values, coupled with a serious lack of cross-referencing/pattern-matching. Consequently, one must develop "data-engines" and "data-mechanics" for multivariable analyses of systems commonly having hundreds or thousands of degrees of freedom. The process is particularly difficult when intersystem assemblies are made of known intrasystem building blocks, such as with modularly constructed oligopeptides and glycopeptides interacting with substrate molecules. In fact, the direction of approach, environmental conditions, and many other interactive relations become very important, especially in the development of kinetic models. Although intersystem dynamics and mechanics are very complex and yield a wealth of understanding, they are more of a holistic approach [1] to modern challenges in theoretical areas. The internal thermodynamics of oligopeptidic secondary and tertiary structural elements is perhaps one of the most challenging aspects of chemistry as a whole, in all of its related subdisciplines.Using this reductionist approach [1] and breaking the problem of secondary and tertiary peptide/protein structure up into its constituent elements, one is able to isolate each, creating and refining them, until they are understood in a form that allows them to be reassembled into a more accurate and holistic picture [2]. This would include the formulation of a set of analytic rules to account for the coupling behavior of all parameters in the system. However, at this point there is litt...

Recycling the Waste: The Development of a Catalytic Wittig Reaction

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Definition of Systematic, Approximately Separable, and Modular Internal Coordinates (SASMIC) for macromolecular simulation

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