On protein

Proteins, like other macromolecules, can be made into monolayers at the air-water interface either by spreading, adsorption, or specific binding. Proteins, while complex polymers, are interesting because of their inherent surface activity and amphiphilicity. There is an increasing body of literature on proteins at liquid interfaces, and here we only briefly discuss a few highlights. 

Taketomi H, Ueda Y and Go N 1975 Studies on protein folding, unfolding, and fluctuations by computer simulation Int. J. Pept. Protein Res. 7 445-59... 

Van Tassel P R, Guemourl L, Ramsden J J, Tar]us G, VIot P and Talbot J 1998 A model for the Influence of conformational change on protein adsorption kinetics J. Colloid Interfaoe Sc/. 207 317-23... 

Gutman M 1986 Application of the laser-induced proton pulse for measuring the protonation rate constants of specific sites on proteins and membranes Methods Enzymol. 127 522-38... 

Loncharich, R.J., Brooks, B.R. The effects of truncating long-range forces on protein dynamics. Proteins 6 (1989) 32 5. 

Direct ligand-protein interactions. Van der Waals and Coulomb energy of interaction of atoms of ligand with atoms on protein. 

PDB file. pdb Protein Data Bank file format for 3D stmcture information on proteins and polynucleotides nmm.rcsb.org 53... 

PDB Research Col-laboratory for Structural Bioinformat-ics (RCSB) macromole-cular structure data on proteins, nucleic acids, protein-nucleic acid complexes, and viruses nu- meric. biblio. -20000 records experi- ments Research Col-laboratory for Structural Bioinformatics online, CD-ROM periodi- cally WU7W.TCsh.0Tg/ pdh/... 

OPTS (Optim i/.ed Potentials for Liquid Simulations) is based on a force field developed by the research group of Bill Jorgensen now at Yale University and previously at Purdue University. Like AMBER, the OPLS force field is designed for calculations on proteins an d nucleic acids. It in troduces non bonded in leraclion parameters that have been carefully developed from extensive Monte Carlo liquid sim u lation s of small molecules. These n on-bonded interactions have been added to the bonding interactions of AMBER to produce a new force field that is expected to be better than AMBER at describing simulations w here the solvent isexplic-... 

The charges used for calculations on proteins are best derived using a suitable fragment for each amino acid fleets the environment within the protein (right), rather than the isolated amino acid (left). 

In computational chemistry it can be very useful to have a generic model that you can apply to any situation. Even if less accurate, such a computational tool is very useful for comparing results between molecules and certainly lowers the level of pain in using a model from one that almost always fails. The MM+ force field is meant to apply to general organic chemistry more than the other force fields of HyperChem, which really focus on proteins and nucleic acids. HyperChem includes a default scheme such that when MM+ fails to find a force constant (more generally, force field parameter), HyperChem substitutes a default value. This occurs universally with the periodic table so all conceivable molecules will allow computations. Whether or not the results of such a calculation are realistic can only be determined by close examination of the default parameters and the particular molecular situation. ... 

While electrospray is used for molecules of all molecular masses, it has had an especially marked impact on the measurement of accurate molecular mass for proteins. Traditionally, direct measurement of molecular mass on proteins has been difficult, with the obtained values accurate to only tens or even hundreds of Daltons. The advent of electrospray means that molecular masses of 20,000 Da and more can be measured with unprecedented accuracy (Figure 40.6). This level of accuracy means that it is also possible to identify post-translational modifications of proteins (e.g., glycosylation, acetylation, methylation, hydroxylation, etc.) and to detect mass changes associated with substitution or deletion of a single amino acid. 

Theie aie only a few fat replacement products based on protein. LITA is a com protein—polysaccharide compound the role of the polysaccharide is to stabilize the protein (zein). The final product is 87% protein and 5% polysaccharide. The mixture, spray dried after processing, claims to look like cream on rehydration. It is low in viscosity, flavor, and lubricity, and is stable to mild heating. The protein particle size is 0.3—3 p.m (55). 

Mechanism of Action. Eew data are available that describe the effects of anaboHc steroids on protein metaboHsm even fewer data exist for assessment of direct effects of anaboHc steroids on Hpid metaboHsm in growing mminants. The lack of any consistent change in somatotropin, prolactin, insulin, or other metaboHc hormones (qv) in a total of 15 studies has been noted (1,38). 

Protein engineering encompasses a vast amount and wide variety of research. At least two textbooks (1,2) have been devoted exclusively to this topic, and several excellent reviews have been pubHshed (3,4). Herein, an overview of principles, an introduction to basic techniques, and a summary of results of representative experiments on protein engineering are provided. 

Disulfides. The introduction of disulfide bonds can have various effects on protein stability. In T4 lyso2yme, for example, the incorporation of some disulfides increases thermal stability others reduce stability (47—49). Stabili2ation is thought to result from reduction of the conformational entropy of the unfolded state, whereas in most cases the cause of destabili2ation is the introduction of dihedral angle stress. In natural proteins, placement of a disulfide bond at most positions within the polypeptide chain would result in unacceptable constraint of the a-carbon chain. 

Uraizee and Narsimhan [Sep. Sci. Technol., 30(6), 847 (1995)] have provided a model for the continuous separation of proteins from dilute solutions. Although their work is focused on protein separation, the model should find general application to other separations. 

Low-molecular-weight products, generally secondary metabolites such as alcohols, carboxyhc and an iino acids, antibiotics, and vitamins, can be recovered using many of the standard operations such as liquid-hquid extraction, adsorption and ion-exchange, described elsewhere in this handbook. Proteins require special attention, however, as they are sufficiently more complex, their function depending on the integrity of a delicate three-dimensional tertiaiy structure that can be disrupted if the protein is not handled correctly. For this reason, this section focuses primarily on protein separations. Cell separations, as a necessary part of the downstrean i processing sequence, are also covered. 

The differences in sizes and locations of hydrophobic pockets or patches on proteins can be exploited in hydrophobic interaction chromatography (HIC) and reversed-pha.se chromatography (RPC) discrimination is based on interactions between the exposed hydro-... 

M. Dungelhoef, M. Rodehutscord, H. Spiekers and E. Pfeffer, Anim. Feed Sci. Technol., 1994,49, 1. M. I. Ferraz de Oliveira and T. Acamovic, in Proceedings of VII Symposium on Protein Metabolism and Nutrition, Evora, Portugal 1995, 1996 in press. 

This chapter lists some representative examples of biochemicals and their origins, a brief indication of key techniques used in their purification, and literature references where further details may be found. Simpler low molecular weight compounds, particularly those that may have been prepared by chemical syntheses, e.g. acetic acid, glycine, will be found in Chapter 4. Only a small number of enzymes and proteins are included because of space limitations. The purification of some of the ones that have been included has been described only briefly. The reader is referred to comprehensive texts such as the Methods Enzymol (Academic Press) series which currently runs to more than 344 volumes and The Enzymes (3rd Edn, Academic Press) which runs to 22 volumes for methods of preparation and purification of proteins and enzymes. Leading referenees on proteins will be found in Advances in Protein Chemistry (59 volumes. Academic Press) and on enzymes will be found in Advances in Enzymology (72 volumes, then became Advances in Enzymology and Related Area of Molecular Biology, J Wiley Sons). The Annual Review of Biochemistry (Annual Review Inc. Patio Alto California) also is an excellent source of key references to the up-to-date information on known and new natural compounds, from small molecules, e.g. enzyme cofactors to proteins and nucleic acids. 

RL Tatusov, EV Koonin, DJ Lipman. A genomic perspective on protein families. Science 278 631-637, 1997. 

WC Barker, MO Dayhoff. Evolution of homologous physiological mechanisms based on protein sequence data. Comp Biochem Physiol [B] 62 1-5, 1979. 

H Taketomi, Y Ueda, N Go. Studies on protein folding, unfolding and fluctuations by computer simulation. 1. The effect of specific ammo acid sequence represented by specific mter-umt interactions. Int J Peptide Protein Res 7 445-459, 1975. 

Alber, T. Mutational effects on protein stability. Annu. Rev. Biochem. 58 765-798, 1989. 

In NMR the magnetic-spin properties of atomic nuclei within a molecule are used to obtain a list of distance constraints between those atoms in the molecule, from which a three-dimensional structure of the protein molecule can be obtained. The method does not require protein crystals and can be used on protein molecules in concentrated solutions. It is, however, restricted in its use to small protein molecules. 

The World Wide Web has transformed the way in which we obtain and analyze published information on proteins. What only a few years ago would take days or weeks and require the use of expensive computer workstations can now be achieved in a few minutes or hours using personal computers, both PCs and Macintosh, connected to the internet. The Web contains hundreds of sites of Interest to molecular biologists, many of which are listed in Pedro s BioMolecular Research Tools (http // www.fmi.ch/biology/research tools.html). Many sites provide free access to databases that make it very easy to obtain information on structurally related proteins, the amino acid sequences of homologous proteins, relevant literature references, medical information and metabolic pathways. This development has opened up new opportunities for even non-specialists to view and manipulate a structure of interest or to carry out amino-acid sequence comparisons, and one can now rapidly obtain an overview of a particular area of molecular biology. We shall here describe some Web sites that are of interest from a structural point of view. Updated links to these sites can be found in the Introduction to Protein Structure Web site (http // WWW.ProteinStructure.com/). 

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