9-Fluorenylmethoxycarbonyl (Fmoc) amino acids were first used for solid phase peptide synthesis a little more than a decade ago. Since that time, Fmoc solid phase peptide synthesis methodology has been greatly enhanced by the introduction of a variety of solid supports, linkages, and side chain protecting groups, as well as by increased understanding of solvation conditions. These advances have led to many impressive syntheses, such as those of biologically active and isotopically labeled peptides and small proteins. The great variety of conditions under which Fmoc solid phase peptide synthesis may be carried out represents a truly "orthogonal" scheme, and thus offers many unique opportunities for bioorganic chemistry.

Solid phase peptide synthesis utilizing 9‐fluorenylmethoxycarbonyl amino acids

The ClusPro server (https://cluspro.org) is a widely used tool for protein-protein docking. The server provides a simple home page for basic use, requiring only two files in Protein Data Bank (PDB) format. However, ClusPro also offers a number of advanced options to modify the search; these include the removal of unstructured protein regions, application of attraction or repulsion, accounting for pairwise distance restraints, construction of homo-multimers, consideration of small-angle X-ray scattering (SAXS) data, and location of heparin-binding sites. Six different energy functions can be used, depending on the type of protein. Docking with each energy parameter set results in ten models defined by centers of highly populated clusters of low-energy docked structures. This protocol describes the use of the various options, the construction of auxiliary restraints files, the selection of the energy parameters, and the analysis of the results. Although the server is heavily used, runs are generally completed in <4 h.

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The ClusPro web server for protein-protein docking.

Publisher Summary This chapter describes the present state of the studies of the molten globule state and its role in protein folding and physiological processes Recent data on the intermediates (equilibrium and kinetic), focusing attention on the molten globule state are discussed in the chapter The molten globule has a native-like overall architecture (folding pattern) without including the rigid packing of side chains It is separated by first-order phase transitions from both the native and the unfolded states and represents a third thermodynamic state of protein molecules It is a universal kinetic intermediate in protein folding; the structure of this intermediate is similar to the structure of the equilibrium molten globule It is predicted and confirmed experimentally that the molten globule state can exist in a living cell and plays an important role in a number of physiological processes

Molten globule and protein folding.

Biopolyesters polyhydroxyalkanoates (PHA) produced by many bacteria have been investigated by microbiologists, molecular biologists, biochemists, chemical engineers, chemists, polymer experts and medical researchers. PHA applications as bioplastics, fine chemicals, implant biomaterials, medicines and biofuels have been developed and are covered in this critical review. Companies have been established or involved in PHA related R&D as well as large scale production. Recently, bacterial PHA synthesis has been found to be useful for improving robustness of industrial microorganisms and regulating bacterial metabolism, leading to yield improvement on some fermentation products. In addition, amphiphilic proteins related to PHA synthesis including PhaP, PhaZ or PhaC have been found to be useful for achieving protein purification and even specific drug targeting. It has become clear that PHA and its related technologies are forming an industrial value chain ranging from fermentation, materials, energy to medical fields (142 references).

A microbial polyhydroxyalkanoates (PHA) based bio- and materials industry

Publisher Summary The chapter discusses the protein stability with emphasis on compact globular proteins representing a single cooperative system. All the small compact globular proteins represent cooperative systems; they exhibit an extreme cooperativity that integrates the whole of their structure into a single structural unit. The large proteins, to which fibrillar proteins are also related, do not present single cooperative systems, but are subdivided into definite cooperative subsystems—structural blocks or domains. The advances in studying the stability of complicated proteins are connected with two methodical achievements: (1) the appearance of the precise scanning microcalorimetric technique, which affords reliable information on the heat capacity function of proteins in a broad temperature range; and (2) realization of the fact that the complicated heat effect of disruption of a complex macromolecular structure can be analyzed thermodynamically. The thermodynamic specificity of collagen has been considered. The volume of globular proteins does not increase at denaturation but decreases, as seen from their ability to denature under high pressure. The results of calorimetric studies are discussed, presenting the specific melting enthalpy of various protein structures—globular proteins, double-stranded coiled coils, and triplestranded coiled coils. The practical importance of thermodynamic studies of protein stability—that is, its importance not only for understanding the principles of organization of these molecules, but just for obtaining structural information on the domain level is emphasized.

Stability of proteins. Proteins which do not present a single cooperative system

Selection of optimum parameters for pulse Fourier transform nuclear magnetic resonance

Rapid scan Fourier transform NMR spectroscopy

In vivo flux between phosphocreatine and adenosine triphosphate determined by two-dimensional phosphorous NMR.

The choice of optimal parameters for measurement of spin-lattice relaxation times. II. Comparison of saturation recovery, inversion recovery, and fast inversion recovery experiments

James A. Ferretti

Papers

Selection of optimum parameters for pulse Fourier transform nuclear magnetic resonance

Rapid scan Fourier transform NMR spectroscopy

In vivo flux between phosphocreatine and adenosine triphosphate determined by two-dimensional phosphorous NMR.

The choice of optimal parameters for measurement of spin-lattice relaxation times. II. Comparison of saturation recovery, inversion recovery, and fast inversion recovery experiments

Expression studies and mutational analysis of the androgen regulated homeobox gene nkx3.1 in benign and malignant prostate epithelium