Finding the optimal solution to a complex optimization problem is of great importance in many fields, ranging from protein structure prediction to the design of microprocessor circuitry. Some recent progress in finding the global minima of potential energy functions is described, focusing on applications of the simple "basin-hopping" approach to atomic and molecular clusters and more complicated hypersurface deformation techniques for crystals and biomolecules. These methods have produced promising results and should enable larger and more complex systems to be treated in the future.

/pdf/global-optimization-of-clusters-crystals-and-biomolecules-2ehy01ydei.pdf

Global optimization of clusters, crystals, and biomolecules

Publisher Summary In the proper environment, a polypeptide chain can fold spontaneously to the three-dimensional structure of a native protein, and despite the possible presence of barriers in conformational space, the chain can find its way around these barriers to reach the structure of lowest free energy. This chapter describes the spontaneous folding of proteins; in vitro complementation of protein fragments; flexibility of proteins in solution: effect of cross-links and ligands, synthetic analogs of proteins; experimental approaches to the study of conformation; and energetic factors determining protein folding. The interatomic interactions within the chain and between the chain and the solvent dictate the folding and the range of the forces involved, is such that near-neighbor interactions are dominant. Folding is envisaged as taking place by the formation of nucleation sites in various parts of the chain, in response to near-neighbor interactions; the various nucleation sites become stabilized, when they are brought into proximity, so that long-range interactions can become operative. However, the development of conformational energy calculation procedures will enable the three-dimensional structure of a native protein to be predicted from the knowledge of its amino acid sequence and its interactions with the solvent in which it is dissolved.

Experimental and theoretical aspects of protein folding.

Bovine whey proteins – Overview on their main biological properties

The protein universe is the set of all proteins of all organisms Here, all currently known sequences are analyzed in terms of families that have single-domain or multidomain architectures and whether they have a known three-dimensional structure Growth of new single-domain families is very slow: Almost all growth comes from new multidomain architectures that are combinations of domains characterized by ≈15,000 sequence profiles Single-domain families are mostly shared by the major groups of organisms, whereas multidomain architectures are specific and account for species diversity There are known structures for a quarter of the single-domain families, and >70% of all sequences can be partially modeled thanks to their membership in these families

https://www.pnas.org/content/pnas/106/27/11079.full.pdf

Nature of the protein universe.

Refined structure of baboon alpha-lactalbumin at 1.7 A resolution. Comparison with C-type lysozyme.

Computation of structures of homologous proteins. .alpha.-Lactalbumin from lysozyme

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Computation of structures of homologous proteins. .alpha.-Lactalbumin from lysozyme