Protein biochemistry

Calculations of the MM type have long been popular in the fields of polymers (12) and biochemistry (proteins) (13), where the huge size of the molecules demands drastic simplification of potential energy functions. These applications are not discussed here. 

Ellis, R.J. (1996a). The bio in biochemistry Protein folding inside and outside the cell. Science 272 1448-1449. 

Shifting from one interdisciplinary nomenclature to another we can view the bidentate molecule as an amino acid, the amide becomes a peptide and the polyamide a polypeptide or a protein. Hence, we have abjured organic chemistry in favour of biochemistry. Proteins are built up from approximately 20-25 different a-amino acids, the individual order of which decide the chemical and physical properties of a particular protein. Due to a combination of certain attributes of e peptide linkage, and the presence of functionalities enabling the formation of hydrogen bonds, protein strands fall into one of three geometrically different categories random coil, a-helix and pleated sheet. 

Stadtman TC. 1974. Selenium biochemistry. Proteins containing selenium are essential components of certain bacterial and mammalian enzyme systems. Science 183 915-921. 

The "bio" in biochemistry protein folding inside and outside the cell, R. J. Ellis, 1996, Science, 272 14481449. 

INTRODUCTION TO BIOCHEMISTRY PROTEINS (SECTIONS 24.6 AND 24.7) Many of the molecules that are essential for life are large natural polymers that are constructed from smaller molecules called monomers. Three of these biopolymers are considered in this chapter proteins, polysaccharides (carbohydrates), and nucleic acids. 

Smith, A. B., and Knowles, C. J., Potential role of a conducting polymer in biochemistry protein binding properties, Biotech. Appl. Biochem., 12, 661-669 (1990). 

Chi Z H, Chen X G, Holtz J S W and Asher S A 1998 UV resonance Raman-selective amide vibrational enhancement quantitative methodology for determining protein secondary structure Biochemistry 27 2854-64... 

The modem era of biochemistry and molecular biology has been shaped not least by the isolation and characterization of individual molecules. Recently, however, more and more polyfunctional macromolecular complexes are being discovered, including nonrandomly codistributed membrane-bound proteins [41], These are made up of several individual proteins, which can assemble spontaneously, possibly in the presence of a lipid membrane or an element of the cytoskeleton [42] which are themselves supramolecular complexes. Some of these complexes, e.g. snail haemocyanin [4o], are merely assembled from a very large number of identical subunits vimses are much larger and more elaborate and we are still some way from understanding the processes controlling the assembly of the wonderfully intricate and beautiful stmctures responsible for the iridescent colours of butterflies and moths [44]. 

Figure C3.1.7. Time-resolved optical absorjDtion data for the Soret band of photo lysed haemoglobin-CO showing six first-order (or pseudo-first-order) relaxation phases, I-VI, on a logaritlimic time scale extending from nanoseconds to seconds. Relaxations correspond to geminate and diffusive CO rebinding and to intramolecular relaxations of tertiary and quaternary protein stmcture. (From Goldbeck R A, Paquette S J, Bjorling S C and Kliger D S 1996 Biochemistry 35 8628-39.)...

Williams S, Causgrove T P, Gilmanshin R, Fang KS, Callender R H, Woodruff WH and Dyer R B 1996 Fast events in protein folding helix melting and formation in a small peptide Biochemistry ZS 691-7... 

McPhalen, C. A., James, M. N. G. Structural comparison of two serine proteinase-protein inhibitor complexes Eglin-C-Subtilisin Carlsberg and CI-2-subtilisin novo. Biochemistry 27 (1988) 6582-6598... 

Besides such textual databases that provide bibhographic information, sequence databases have attained an even more important role in biochemistry. Sequence databases are composed of amino add sequences of peptides or proteins as well as nudeotide sequences of nudeic acids. The 20 amino adds are mostly represented by a three-letter code or by one letter according to the biochemical conventions) the four nudeic adds are defined by a one-letter code. Thus the composition of a biochemical compound is searchable by text retrieval methods. 

The SWISS-PROT database [36] release 40.44 (February, 2003) contains over 120 000 sequences of proteins with more than 44 million amino adds abstracted from about 100 000 references. Besides sequence data, bibHographical references, and taxonomy data, there are highly valuable annotations of information (e.g., protein function), a minimal level of redundancy, and a high level of integration with other databases (EMBL, PDB, PIR, etc.). The database was initiated in 1987 by a partnership between the Department of Medicinal Biochemistry of the University of Geneva, Switzerland, and the EMBL. Now SWISS-PROT is driven as a joint project of the EMBL and the Swiss Institute of Bioinformatics (SIB). 

As m most aspects of chemistry and biochemistry structure is the key to function We 11 explore the structure of proteins by first concentrating on their fundamental building block units the a ammo acids Then after developing the principles of peptide structure we 11 see how the insights gamed from these smaller molecules aid our under standing of proteins... 

Dill, KA. Theory for the folding and stability of globular proteins. Biochemistry 24 1501-1509, 1985. 

This experiment provides a nice example of the application of spectroscopy to biochemistry. After presenting the basic theory for the spectroscopic treatment of protein-ligand interactions, a procedure for characterizing the binding of methyl orange to bovine serum albumin is described. 

PVDF-based microporous filters are in use at wineries, dairies, and electrocoating plants, as well as in water purification, biochemistry, and medical devices. Recently developed nanoselective filtration using PVDF membranes is 10 times more effective than conventional ultrafiltration (UF) for removing vimses from protein products of human or animal cell fermentations (218). PVDF protein-sequencing membranes are suitable for electroblotting procedures in protein research, or for analyzing the phosphoamino content in proteins under acidic and basic conditions or in solvents (219). 

S. B 2ick cn2cn, Mmino Mcid Determination Methods and Techniques, Marcel Dekker, New York, 1968 A. Niederweiser and G. Pataki, eds., Neiv Techniques in Mmino Mcids, Peptide and Protein Mnalysis, Ann Arbor Science Pubhshers, Ann Arbor, Mich., 1971 The Chemical Society of Japan, eds., Neiv Experimental Chemistry Series, Vol. 1 (Biochemistry 1) (in Japanese), Mamzen, Tokyo, Japan, 1978, pp. 141—160. 

P. L. Privalov, Physical Basis ofi the Stability ofi the Folded Conformations ofi Proteins Protein Folding, Freeman, New York, 1992 K. A. DiU, Biochemistry 29, 7133 (1990). 

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