Peptide in solution

Hermans, J., Yun, R. H., Anderson, A. G. Precision of free-energies calculated by molecular dynamics simulations of peptides in solution. J. Comp. Chem. 13 (1992) 429-442... 

Chirooptical properties give more subtle information on the conformational behavior of biopolymers and peptides in solution. In early experiments, optical rotation and optical rotatory dispersion (ORD) have been recognized as valuable techniques, followed more recently by significant progress and refinements in the equipment which have resulted in the routine measurements of applied circular dichroism (CD). 

From the standard thermochemical data ArG° = (—371.3 — 379.9 + 733.9) kJ mol-1 = —17.3 kJmol-1, corresponding to an equilibrium constant K = 1.1 x 103 M-1. This is a worrying result because all peptides in solution at 298 K should spontaneously fall apart to the monomers and hence all proteins are subject to degradation due to spontaneous hydrolysis. Fortunately, the reaction is kinetically hindered, which means that it occurs very slowly. Kinetics always control the rate at which equilibrium is achieved, relating the ratio of the forward and backward rate constants to the equilibrium constant ... 

Daidone, I., Amadei, A., and Di Nola, A. (2005). Thermodynamic and kinetic characterization of a beta-hairpin peptide in solution An extended phase space sampling by molecular dynamics simulations in explicit water. Proteins 59, 510-518. 

S Sakakibara. Synthesis of large peptides in solution. Biopolymers (Pept Sci) 31, 17, 1995. 

H Kuroda, Y-N Chen, T Kimura, S Sakakibara. Powerful solvent systems useful for synthesis of sparingly-soluble peptides in solution. Ini J Pept Pmt Res 40, 294, 1992. 

For the synthesis of a small library of palmitoylated and isoprenylated N-Ras peptides in solution, a modular strategy was adopted, with the tetrapeptide MGLP 38 as a key intermediate. This tetrapeptide allowed further elongation at its C-terminus with lipidated or nonlipidated cysteine methyl esters, as well as the addition of various N-terminally MIC-labeled dipeptides, consisting of different GC lipidated units 39—41... 

In 2005 Schmidt and coworkers published a reversed approach for synthesizing palmitoylated and farnesy-lated peptides in solution via an S]sr2 displacement of a bromide, which was embedded in a bromoalanine-containing sequence. Thiol-bearing lipids can act as nucleophiles, for example, thiopalmitic acid or farnesylmercaptane. The method gives access to famesylated, palmitoylated, and doubly lipidated peptides (Scheme 17). 

Synthesis of peptides in solution using the method outlined above, or alternative procedures, is laborious... 

For the synthesis of peptides in solution with sulfated hydroxyamino acids as synthons A -Boc protection has been used. Coupling steps are accomplished with DCC using HOBt or pentafluorophenol as additives, and identical coupling procedures are applied for the... 

Complexes of other amino acids or their derivatives with cobalt(II) that have been investigated include dipeptides (120) these complexes have long been known to absorb dioxygen. For example, the mononuclear cobalt(II) complex of N, N,N", N "-diglycylethylenediaminete-traacetic acid (121) absorbs one mole of dioxygen per two moles of complex. This system has been proposed as a simple, convenient model system for the study of dioxygen complexes of cobalt(II) peptides in solution because of its relatively slow conversion to the irreversibly formed cobalt(III) dioxygen complex. 

In my talk I surveyed recent advances in the methodology and selected 2D-IR spectra of secondary structures. The results promise to provide structurally based kinetic probes for conformational dynamics, sharp tests of anharmonic potential surfaces and novel information regarding the transient and equilibrium vibrational dynamics of peptides. The heterodyned 2D-IR approach has proven useful in determining structures of peptides in solution and the anharmonic nature of the potential surfaces of peptides and secondary structures [1-10], as have polarized photon echo [2,6,10-12] or pump-probe techniques [4,13-16]. 

Proline is an exceptional amino acid residue in that the cis-trans equilibrium only slightly favors the trans form in peptidyl-proline bonds. Small proline-containing peptides in solution contain some 5 to 30% of the cis (syn) isomer, as opposed to less than 0.1% of the cis isomers of the other amino acids.14 The cis form is even found in native proteins two of the four prolines in ribonuclease A... 

Enzyme activities are based on rates of casein hydrolysis under defined conditions. The products of casein hydrolysis, as defined in this protocol, are those peptides soluble in 5% TCA that can be detected by the bicinchoninic acid (BCA) protein assay (unitbi.i). The amount of TCA-soluble peptide generated during the course of the reaction can actually be quantified by any one of several protein/peptide assays. The color yield in these assays is assumed to be proportional to the amount of peptide in solution. The amount of product/peptide in the reaction mixture is often reported as bovine serum albumin (BSA) equivalents—since standard curves based on this protein may be used to calibrate the assay. Thus, activity units can be expressed as the amount of BSA equivalents generated per unit time. 

Many methods are available for measuring TCA-soluble peptides. Possibly the easiest is to measure the absorbance of the solution at 280 nm, as the absorbance at this wavelength is a function of the aromatic amino acid content of the solution. This approach requires a UV spectrophotometer, and the sensitivity of the assay is likely to be lower than that of some of the colorimetric assays. There are also several colorimetric peptide assays that can be applied to this type of peptidase assay, such as the Biuret, Lowry, and Bradford dye-binding methods (for comparison see Piyachomkwan and Penner, 1995). All of these methods measure a relative value rather than an absolute amount of peptide in solution. The results should thus be reported in terms of equivalents, such as BSA equivalents when using a calibration curve prepared using a BSA standard solution. 

More recent advances in the synthesis of head-to-tail cyclic peptides combine solid-phase peptide synthesis with solid-phase cyclization reactions whilst the peptide is still attached to the resin. 25 Such methods have obvious merits as they reduce manipulation of the peptides in solution. The method typically requires a suitable side-chain functional group... 

The inactivity of acidic proteinoid (A) synthesize peptides in solution of pH 7.2 is in contrast to the activity of the lysine-rich proteinoid (B), when A and B form microspheres. The activity of the complex is several times as large as that of lysine-rich proteinoid alone 28). Physical surface and interior providing suitable environment for dehydration may be responsible. It may also be that the closed molecules of both proteinoids may be opened by the interaction, consequently buried active sites of proteinoids become effective. Neutral amino acids contained in each proteinoid may prevent the entire neutralization of acidic and basic residues. In the synthetic pathways of peptides and oligonucleotides by proteinoid microspheres, proteinoid nucleotide complex is proposed in this article as a main intermediate of the reactions. Oligo-... 

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