Peptides/polypeptides conformational analysis

The wavelengths of IR absorption bands are characteristic of specific types of chemical bonds. In the past infrared had little application in protein analysis due to instrumentation and interpretation limitations. The development of Fourier transform infrared spectroscopy (FUR) makes it possible to characterize proteins using IR techniques (Surewicz et al. 1993). Several IR absorption regions are important for protein analysis. The amide I groups in proteins have a vibration absorption frequency of 1630-1670 cm. Secondary structures of proteins such as alpha(a)-helix and beta(P)-sheet have amide absorptions of 1645-1660 cm-1 and 1665-1680 cm, respectively. Random coil has absorptions in the range of 1660-1670 cm These characterization criteria come from studies of model polypeptides with known secondary structures. Thus, FTIR is useful in conformational analysis of peptides and proteins (Arrondo et al. 1993). 

Because our research is focused on problems relevant to secondary structure of proteins in solution, this section will briefly review the recent developments in spectroscopic techniques applied to this problem. These techniques are considered low-resolution methods which provide global insight into the overall secondary structure of proteins without being able to establish the precise three-dimensional location of individual structural elements [707], Vibrational spectroscopy has played a pioneering role in studying the conformations of peptides, polypeptides, and proteins [702]. The advent of stable and powerful lasers has led to the development of Fourier transform methods which allows the use of powerful computational techniques for the analysis of spectral data [10,103,104], Laser... 

The liquid phase synthesis on PEG has also been used for the conformational analysis of collagen-like sequences by CD studies 237). The attachment to PEG has also permitted the CD spectral delineation of the specific interactions between the polypeptide chains and sidechain groups 238,239). Thus, Anzinger et al. observed that onset of local ordered structures in the mesogenic side chains of polylysine blocks attached to PEG leads to significant, specific alteration in the backbone conformations of the peptide chain 239). 

Anderson GJ. Circular dichoism and Fourier transform infra-red analysis of polypeptide conformation. In Reid RE, ed. Peptide and Protein Drug Analysis. New York Marcel Dekker, 2000 753-774. 

P. W. Schiller, The use of steady-state fluorescence techniques in the conformational analysis of polypeptides in Perspectives in Peptide chemistry (A. Eberle, R. Geiger, Th. Wieland eds.) S. Karger, Basel 1981, pp. 236-248... 

Ciarkowski et al have compared two variants - AMBER/8 flP03 versus ECEPP/3 - of NMR based (including /hohn couplings) conformational analysis. It appears that the AMBER/8 ensembles obtained for two flexible peptides have much smaller standard deviations in /-couplings than those obtained for the ECEEP ones. Table 1 contains polypeptide chains whose structures were solved with the aid of vicinal proton-proton couplings. 

TTie C-terminal polypeptide block A (residues 462-497) has also been synthesized and its three dimensional structure in solution (90% H2O/10%D2O) was determined by two-dimensional NMR-spectroscopy with a 600 MHz instrument 28. According to this analysis the peptide has a wedge-like shape with dimensions 3 x 1.8 x 1.0 nm. This wedge probably represents the last part in the SAXS model which has a length of about 4 nm and a maximum diameter of 1.4 nm. The principle element of the secondary structure in this part is the conformation. Three antiparallel short jS-sheets composed of residues 466 to 470 ()5j), 485 to 489 and 493 to 496... 

Wehr, C. T. (1991). Post column reaction systems for fluorescence detection of polypeptides. In High-Performance Liquid Chromatography of Peptides and Proteins Separation, Analysis, and Conformation (C. T. Mant and R. S. Hodges, eds.), pp. 579-586. CRC Press, Boca Raton, FL. 

Since the dispersive properties of helices in what will be taken as the standard sense, now known to be right-handed as in myoglobin, have been the most thoroughly studied and since a case can be made that it is the predominant sense in proteins, this review will focus on the capacity of optical rotatory methods to discern mixtures of this conformation with disordered regions. It will discuss the manner in which theoretical considerations have provided the forms into which rotatory data are currently cast, the calibration of their constants by studies of synthetic polypeptides in known conformation, and then the application of these equations and scales in the structural interpretation of the rotatory dispersion of proteins. This pattern of analysis will undoubtedly undergo refinement and revision as these methods are applied to new species of polypeptide and protein in concert with other means of conformational assignment. In particular, an extension of the spectral range of measurement toward optically active absorption bands in the far ultraviolet can be expected to yield new information about the rotatory power of the peptide bond and thus enhance the interaction of theory and observation that has already proved fruitful. 

This conclusion was reached, tentatively, by Frenkel, Shaltyko and Elyashevich A phenomenological analysis presented by Pincus and de Gennes predicted a first-order phase transition even in the absence of cooperativity in the conformational transition. These authors relied on the Maier-Saupe theory for representation of the interactions between rodlike particles. Orientation-dependent interactions of this type are attenuated by dilution in lyotropic systems generally. In the case of a-helical polypeptides they should be negligible owing to the small anisotropy of the polarizability of the peptide unit (cf. seq.). Moreover, the universally important steric interactions between the helices, regarded as hard rods, are not included in the Maier-... 

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