Peptides geometry

In effect, protein structure determination is a search for the conformation of a molecule whose chemical composition is known. For this reason, conformational angles about single bonds are not constrained during refinement, and they should settle into reasonable values. Spectroscopic evidence abundantly implies that peptide bonds are planar, and some refinements constrain peptide geometry. If unconstrained, peptide bonds should settle down to within one to two degrees of planar. 

As illustrated by the synthesis of 13, which can be viewed as a Gly-Hse (Hse = homoserine) mimic (Scheme 1.2.4), aminals of the general structure 11 serve as versatile educts for the preparation of pipecolyl-dipeptide analogs with fixed anti-peptide geometry. The stereochemistry of compound 13 was determined unambiguously by 2D NOESY NMR spectroscopy and is in accordance with a re-... 

Perricaudet and Pullman52) have also done an ab initio study which suggests that a small amount of twisting about the C—N bond (up to about 15°) can occur with very little loss of energy. It should be noted that the structural parameters in both of these studies were based on an average peptide geometry, not on experimental structural parameters determined particularly for NMA. 

High temperature searches of conformational space (see Quenched Dynamics" on page 78), can produce unwanted conformational changes, such as cis-tmnx peptide flips, ring inversions, and other changes that you cannot reverse easily by geometry optimization. You can use restraints to prevent these changes. 

Some of the other features of this program are the ability to compute transition states, coordinate driving, conformation searches, combinatorial tools, and built-in visualization. The builder includes atoms and fragments for organics, inorganics, peptides, nucleotides, chelates, high-coordination geometries, and... 

Our reviewer felt the molecule builder was easy to use. It is set up for organic molecules. Specialized building modes are available for peptides, nucleotides, and carbohydrates. It is also possible to impose constraints on the molecular geometry. Functions are accessed via a separate window with buttons labeled with abbreviated names. This layout is convenient to use, but not completely self-explanatory. The program is capable of good-quality rendering. At the time of this book s publication, a new three-dimensional graphic user interface called Maestro was under development. 

The geometry of the peptide bond is planar and the mam chain is arranged m an anti conformation (Section 27 7)... 

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. 

As a consequence of their different turn geometry a 10-membered turn closed by H-bonds between NH and C=0 +i and a 12-membered turn closed by Id-bonds between C=0 and NH +3, antiparallel hairpins formed by y9-peptides 121 and 122 display opposite sheet polarities (see Fig. 2.30A and B). Comparison of backbone torsion angles (X-ray and NMR) for selected y9-amino acids residues within extended strand segments of peptides 117-122 are shown in Tab. 2.7. The observed values are close to ideal values for y9-peptide pleated sheets =-120° (or 120°), 01 = 180°, (/ =120°(or-120°). 

The characteristic coiled-coil motifs found in proteins share an (abcdefg) heptad repeat of polar and nonpolar amino acid residues (Fig. 1). In this motif, positions a, d, e, and g are responsible for directing the dimer interface, whereas positions b, c, and f are exposed on the surfaces of coiled-coil assemblies. Positions a and d are usually occupied by hydrophobic residues responsible for interhelical hydrophobic interactions. Tailoring positions a, d, e, and g facilitates responsiveness to environmental conditions. Two or more a-helix peptides can self-assemble with one another and exclude hydrophobic regions from the aqueous environment [74]. Seven-helix coiled-coil geometries have also been demonstrated [75]. 

Adamski, RP Anderson, JL, Configurational Effects on Polystyrene Rejection from Micro-porosou Membranes, Journal of Polymer Science Part B Polymer Physics 25, 765, 1987. Adler, PM, Porous Media, Geometry and Transports Butterworth-Heinemann Boston, 1992. Afeyan, NB Fulton, SP Regnier, FE, Perfusion Chromatography Packing Materials for Proteins and Peptides, Journal of Chromatography 544, 267, 1991. 

C13-0116. The nitrogen atom of a peptide linkage has trigonal planar geometry. What is the hybridization of the nitrogen atom in a peptide linkage Explain why nitrogen adopts this form of hybridization. 

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