Peptides properties

Y. Wang. Computational Approach to the Influence of the Distdfl.dc Bond on Peptide Properties. PhD thesis. University of Kansas, 1997. 

Cyclic peptides are important biologically active compounds that combine peptide properties with conformational bias and often improved serum stability and membrane penetration [1-3]. Depsipeptides are similar compounds, but they contain as part of their backbone one or more hydroxylated amino acid residues that add ester or lactone moieties to the peptide (Fig. 1) [4-6]. Cyclo- and... 

The potential utility of peptides as therapeutic agents with clinical applications is limited as a consequence of intrinsic peptide properties such as metabolic instability or poor transmembrane mobility. Hence, the design and synthesis of meta-bolically stable peptide analogs that can either mimic or block the bioactivity of natural peptides or enzymes is an important area of medicinal chemistry research. Numerous structural modifications to peptides have been examined in pursuit of molecules with more desirable properties [1-3]. These modified structures, peptidomimetics, are nonpeptide molecules that imitate the desired properties of the natural substances. 

The study of Saa has so far concentrated on their use as biopolymer building blocks to mimic oligo- and polysaccharide structures via amide bond linkages.1In 1994 the first example of a Saa as a new type of peptidomimetic [replacement of amino acid(s) by Saa] was reported/44 which was later extended to the Saa construction kit 7-16, and others, a versatile tool for the manipulation of peptide properties 45"51 (Scheme 2). 

A later study using the same data set of 20 peptides showed that similar results could be obtained using a set of three descriptors, z values, based on an earlier analysis of changes in peptide properties due to amino acid substitutions. These were found using principal component analysis (75) of the effects of... 

This type of carbohydrate mimetic was coined saccharide-peptide hybrid to point out that carbohydrate properties as well as peptide properties are represented. The mimetics still retain the carbohydrate epitopes available for binding, the p)ranose or furanose ring plus hydroxy groups, as well as the peptide function. 

The potential of using other peptide properties to support the identification was evaluated. Parameters such as retention time [24-25] or isoelectric point (pi) [104, 153] were evaluated for this purpose. 

In general, the first step in virtual screening is the filtering by the application of Lipinski s Rule of Five [20]. Lipinski s work was based on the results of profiling the calculated physical property data in a set of 2245 compounds chosen from the World Drug Index. Polymers, peptides, quaternary ammonium, and phosphates were removed from this data set. Statistical analysis of this data set showed that approximately 90% of the remaining compounds had ... 

Hagler A T and S Lifson 1974. Energy Functions for Peptides and Proteins. II. The Amide Hydrogen Bond and Calculation of Amide Crystal Properties. Journal of the American Chemical Society 96 5327-5335. 

Individual ammo acids differ m their acid-base properties This is important m peptides and proteins where the properties of the substance depend on its ammo acid constituents especially on the nature of the side chains It is also important m analyses m which a complex mixture of ammo acids is separated into its components by taking advantage of the differences m their proton donating and accepting power... 

Electrophoresis is used primarily to analyze mix tures of peptides and proteins rather than individual ammo acids but analogous principles apply Because they incorporate different numbers of ammo acids and because their side chains are different two pep tides will have slightly different acid-base properties and slightly different net charges at a particular pH Thus their mobilities m an electric field will be differ ent and electrophoresis can be used to separate them The medium used to separate peptides and proteins is typically a polyacrylamide gel leading to the term gel electrophoresis for this technique... 

Section 27 20 The folding of a peptide chain is its tertiary structure The tertiary struc ture has a tremendous influence on the properties of the peptide and the biological role it plays The tertiary structure is normally determined by X ray crystallography... 

The temperature of a simulation depends on your objectives. You might use high temperatures to search for additional conformations of a molecule (see Quenched Dynamics on page 78). Room temperature simulations generally provide dynamic properties of molecules such as proteins, peptides, and small drug molecules. Low temperatures (<250 K) often promote a molecule to a lower energy conformation than you could obtain by geometry optimization alone. 

Peptides and proteins are formed by linking successive amino acids into chains or rings. The order (sequence) and types of amino acids determine the chemical and physical properties of peptides and proteins. 

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