Zwitterions peptides

To illustrate the potential of the three-layer ONIOM method, we show results from a systematic comparison of three- and two-layer ONIOM methods with full QM benchmark calculations [11], The system studied is a zwitterionic peptide, NH3+—CHnBu—CO—NH—CH2—CO—NH—CH Bu—COO-, and the partition scheme illustrated in Figure 2-2 is used. In this partition, both model and mid... 

The conformational angles derived in this study are unusual values in the Ramachandran map because these maps are based on conformational energy calculations for molecules as N-acetyl-alanine-N -methyl amide, which do not incorporate charged groups and thus will reproduce an uncharged peptide fragment better than an aqueous solution of a zwitterionic peptide. 

We believe that addition of salts to water will alter the peptide behavior to a large extent, because the charged groups in the side chains are screened by counterions. Behavior of the zwitterionic peptide could be significantly different from that of the un-ionized one, since the charged N- and C-termini can interact with the charged groups of the side chains. We emphasize that these are not true in the case of Met-enkephalin. 

FIGURE 10.6 Schematic representation of selective enzyme-triggered charge-induced swelling of the enzyme-responsive hydrogels with the zwitterionic peptide linkers that are hydrolyzed by a specific enzyme. 

Morokuma, K., Wang, Q., 8c Vreven, T. (2006). Performance evaluation of the three-layer ONIOM method Case study for a zwitterionic peptide. Journal of Chemical Theory and Computation, 2, 1317-1324. 

The p-nitrophenol fonned as a byproduct in this reaction is easily removed by extraction with dilute aqueous base. Unlike free amino acids and peptides, protected peptides are not zwitterionic and are more soluble in organic solvents than in water. 

Proteins are large biomolecules made up of a-amino acid residues linked together by amide, or peptide, bonds. Chains with fewer than 50 amino acids are often called peptides, while the term protein is reserved for larger chains. Twenty amino acids are commonly found in proteins all are a-amino acids, and all except glycine have stereochemistry similar to that of l sugars. In neutral solution, amino acids exist as dipolar zwitterions. 

FIG. 9 A scheme representing lateral phase separation for anionic lipids from zwitterionic lipids in a mixed lipid bilayer induced by the peptide antibiotic, polymyxin-B. (Reprinted by permission from Ref. 41, copyright 1998, Elsevier Science.)... 

Fig. 3 Protonation states, isomerism and mesomerism of the HBI chromophore (p-hydroxybenzi-lidene-imidazolinone). The chromophore is shown in its most stable Z ( cw ) conformation, conventionally associated to a 0° value of the dihedral angle t, while the E ( trans ) conformation corresponds to t = 180°. For model compound HBDI (4 -hydroxy-benzylidene-2,3-dimethyl-imidazolinone), Ri = R2 = CH3, for chromophore in GFP, Ri, and R2 stand for the peptidic main chains toward N-terminus and C-terminus, respectively, (a) Possible protonation states of HBI (a) neutral, (b) anionic, (c) enolic, (d) cationic, and (e) zwitterionic. (b) Two resonance structures of the anionic form of HBI...

A novel natural product has been isolated from the Micronesian sponge Dysidea herbacea. This material is the zwitterionic pyrroloimidazopyridine 293 and is claimed to be the first example of a simple peptide with an N,N-aminal linkage <2004JOC1180>. 

Figure 4.1 The zwitterionic structure of two ot-amino acids, and the condensation reaction to form a dipeptide, linked by a peptide bond.

Nilsson KPR, Rydberg J, Baltzer L, Inganas O (2003) Self-assembly of synthetic peptides control conformation and optical properties of a zwitterionic polythiophene derivative. Proc Natl Acad Sci 100 10170-10174... 

Nilsson et al. designed an experiment to test the ability of a polymer to directly detect conformational changes within peptide/protein structure [27]. Using the zwitterionic polythiophene derivative, POWT, they succeeded in detecting the distinct conformations of synthetic peptides. The mechanism was concluded to be based on the polymer side chains charged interactions and hydrogen bonding with the proteins. 

Detergents commonly used to form micelles that are amenable to high-resolution NMR are summarized in Tab. 5.2, and the chemical structures of the most commonly used detergents are presented in Fig. 5.2. Unfortunately, only a few of those needed for use with nonisotopically enriched peptides are commercially available in deuterated form. Most frequently, the zwitterionic DPC or the negatively charged SDS have been used as membrane mimetics. Mixtures of DPC doped with small amounts of SDS may be used to modulate the charge distribution on the micelle surface. It should be emphasized here... 

At its isoelectric point, histidine is said to be zwitterionic, as it has both anionic and cationic properties. Most other amino acids are also zwitterionic at neutral pH. Peptides and proteins also have isoelectric points, which can vary widely depending on the composition of the amino acids. 

Amino acids and peptides in their compounds with alkali metal salts are in the zwitterion form. The anion is hydrogen bonded to the NHs+... 

Figure 14.14 A zwitterionic collagen-like peptide is shown to self-assemble into relative thick fibers displaying a native collagen-like D-spacing pattern. Reprinted from Rele et al. (2007). Copyright 2007 American Chemical Society.

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