Polypeptides in aqueous solution

Vitalis, A., Pappu, R.V. ABSINTH a new continuum solvation model for simulations of polypeptides in aqueous solutions. J. Comput. Chem. 2009, 30, 673-99. 

TAM Tamura, T., Yamaoka, T., Kimugi, S., Panitch, A., and Tirrell, D.A., Effects of temperature and pressme on the aggregation properties of an engineered elastin model polypeptide in aqueous solution. Biomacromolecules, 1, 552, 2000. 

S.M. McDonald, J.W. Brady, and P. Clancy, Molecular dynamics simulations of a winter flounder "antifreeze" polypeptide in aqueous solution, Biopolyniers, 33 (1993) 1481. 

Raman optical activity is an excellent technique for studying polypeptide and protein structure in aqueous solution since, as mentioned above, their ROA spectra are often dominated by bands originating in the peptide backbone that directly reflect the solution conformation. Furthermore, the special sensitivity of ROA to dynamic aspects of structure makes it a new source of information on order-disorder transitions. 

Kallenbach and co-workers have recently demonstrated via CD spec-tropolarimetry and NMR spectrometry that a seven-residue alanine peptide adopts predominantly the PPII helical conformation in aqueous solution (Shi et al., 2002). Since alanine is nothing but backbone, such a finding indicates that the polypeptide backbone possesses an intrinsic... 

Chapman et al. [131] reported the synthesis of poly(ethylene oxide) (PEO) supported dendritic f-BOC-poly(a, c-L-lysines). These dendritic polymers termed as hydramphiphiles formed foams possessing good temporal stability in aqueous solution. Scrimin et al. [132] synthesized a three-directional polypeptide having uses in membrane permeability modulation. Decapeptide fragments were linked to TREN [tris(2-aminoethyl)amine] core. 

Another potential site of reactivity for anhydrides in protein molecules is modification of any attached carbohydrate chains. In addition to amino group modification in the polypeptide chain, glycoproteins may be modified at their polysaccharide hydroxyl groups to form ester derivatives. Esterification of carbohydrates by acetic anhydride, especially cellulose, is a major industrial application for this compound. In aqueous solutions, however, esterification may be a minor product, since the oxygen of water is about as strong a nucleophile as the hydroxyls of sugar residues. 

Transition metals such as iron can catalyze oxidation reactions in aqueous solution, which are known to cause modification of amino acid side chains and damage to polypeptide backbones (see Chapter 1, Section 1.1 Halliwell and Gutteridge, 1984 Kim et al., 1985 Tabor and Richardson, 1987). These reactions can oxidize thiols, create aldehydes and other carbonyls on certain amino acids, and even cleave peptide bonds. The purposeful use of metal-catalyzed oxidation in the study of protein interactions has been done to map interaction surfaces or identify which regions of biomolecules are in contact during specific affinity binding events. 

The Lys-25 polymer was crosslinked into a gel by treatment of a 5% (w/v) solution of the polypeptide in either aqueous phosphate buffer (pH 9) or anhydrous dimethylsulfoxide with a bis(A -hydroxysuccinimidyl) derivative of suberic acid. The reagents were mixed at 4°C, and the solutions were warmed to 25°C. After approximately 10 minutes, the solutions formed mechanically stable gels that could be physically manipulated. The gels formed in DMSO were optically transparent in contrast to the opaque gels formed in aqueous solution. 

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