Unordered conformation

Table 3.3. CD features for a-helix, -sheet and random (i.e. conformations unordered)...

Abstract. A model of the conformational transitions of the nucleic acid molecule during the water adsorption-desorption cycle is proposed. The nucleic acid-water system is considered as an open system. The model describes the transitions between three main conformations of wet nucleic acid samples A-, B- and unordered forms. The analysis of kinetic equations shows the non-trivial bifurcation behaviour of the system which leads to the multistability. This fact allows one to explain the hysteresis phenomena observed experimentally in the nucleic acid-water system. The problem of self-organization in the nucleic acid-water system is of great importance for revealing physical mechanisms of the functioning of nucleic acids and for many specific practical fields. 

The hydration shell is formed with the increasing of the water content of the sample and the NA transforms from the unordered to A- and then to B form, in the case of DNA and DNA-like polynucleotides and salt concentrations similar to in vivo conditions. The reverse process, dehydration of NA, results in the reverse conformational transitions but they take place at the values of relative humidity (r.h.) less than the forward direction [12]. Thus, there is a conformational hysteresis over the hydration-dehydration loop. The adsorption isotherms of the NAs, i.e. the plots of the number of the adsorbed water molecules versus the r.h. of the sample at constant temperature, also demonstrate the hysteresis phenomena [13]. The hysteresis is i( producible and its value does not decrease for at least a week. 

We consider a finite space, which contains the NA sample and is in contact with a bath of water or water vapor. That allows one to maintain the r.h. in the experimental space at a constant level and change it when necessary. Such a scheme corresponds to the real experiments with wet NA samples. A NA molecule is simulated by a sequence of units of the same type. Thus, in the present study, we consider the case of a homogeneous NA or the case where averaging over the unit type is possible. Every unit can be found in the one of three conformational states unordered. A- or B- conformations. The units can reversibly change their conformational state. A unit corresponds to a nucleotide of a real NA. We assume that the NA strands do not diverge during conformational transitions in the wet NA samples [18]. The conformational transitions are considered as cooperative processes that are caused by the unfavorable appearance of an interface between the distinct conformations. 

Let us introduce the variables which are the probabilities of finding an arbitrary nnit in a certain conformational state U for unordered state, A for A- and B for B-form of the NA. There is the natural relationship between the variables ... 

Before discussing details of their model and others, it is useful to review the two main techniques used to infer the characteristics of chain conformation in unordered polypeptides. One line of evidence came from hydrodynamic experiments—viscosity and sedimentation—from which a statistical end-to-end distance could be estimated and compared with values derived from calculations on polymer chain models (Flory, 1969). The second is based on spectroscopic experiments, in particular CD spectroscopy, from which information is obtained about the local chain conformation rather than global properties such as those derived from hydrodynamics. It is entirely possible for a polypeptide chain to adopt some particular local structure while retaining characteristics of random coils derived from hydrodynamic measurements this was pointed out by Krimm and Tiffany (1974). In support of their proposal, Tiffany and Krimm noted the following points ... 

Studies of the secondary structure of cucurbitin have shown its conformational modes consist of 5% a-helical, 32% pleated sheet, and 62% unordered structures (48). These values are similar in distribution to those of oTFfer oilseed globulins (48). 

The three-dimensional conformation of a protein, made up of secondary structural elements and unordered sections, is referred to... 

The exchange data could be fit just as well by the CD-derived parameters with a kint about 17% lower than the value used in the fit to exchange rate data alone. In the latter case, /cint was taken to be the same as the rate of exchange observed for an NH group in an unstructured peptide. It is quite plausible that a peptide NH in a partially helical peptide may differ from that in a completely unstructured peptide. Thus, these results indicate that if the CD parameters are carefully determined for the helical and the unordered conformations, the helix content of peptides can be determined accurately, in agreement with alternative measurements by exchange kinetics. 

UV resonance Raman study of betanova, while consistent with a (3-sheet secondary structure, provides no evidence for a cooperative thermal transition 223 The CD spectra reported by Boyden and Asher 223 showed no indication of (3-sheet features, even at 0 °C, and were indicative of an unordered conformation. It has been suggested 115,223 that the CD in the 220 nm region is dominated by aromatic side-chain contributions, yet the resonance Raman data suggest a molten globule-like structure, which appears inconsistent with substantial CD contributions from aromatic side chains 224 ... 

Many peptides have no well-defined conformation, but exist as an ensemble of conformers, especially in aqueous solution. Unordered peptides have a characteristic strong negative CD band in the 195-200 nm region and a weaker feature in the 220 nm region that may be either positive or negative [shown in Figure 9 for poly(Lys) 94] poly(Ser) 150l and poly(Lys-Leu)192 ]. 

The distribution of conformers in the unordered conformation depends on the amino acid sequence and on the solvent and temperature. However, there is a substantial body of evidence 151 that poly(Pro)II-like conformers are present at significant levels in unordered peptides at room temperature, and become increasingly important as the temperature decreases. This was first pointed out by Tiffany and Krimm/152 who noted the striking similarity of the CD spectra of ionized poly(Lys) and poly(Glu) to that of poly(Pro)II. The spectra are indeed very similar, if one allows for a red shift of -10 nm in the poly(Pro)II spectrum, attributable to the difference between tertiary and secondary amides. The case for poly(Pro)-Il-like conformers in unordered peptides is greatly strengthened by observations that the vibrational CD spectrum of unordered peptides is qualitatively like that of poly(Pro)Il 153 154 ... 

The contribution of the poly(Pro)II conformation to the ensemble of unordered peptides has been considered.1158 The temperature dependence of [0]222 for the peptide Ac-YEAAAKEAPAKEAAAKA-NH2 in 8 M guanidinium chloride and of poly(Lys) in water and in ethylene glycol/water (2 1) mixtures 156 was fitted to a two-state equation for a poly(Pro)II-unordered equilibrium with a temperature-independent AH and temperature-independent molar ellipticities for the two components. The peptide with a Pro at the central position is an unordered peptide, the spectrum of which has pronounced poly(Pro)II-like features at low temperatures. This fit yielded [0]222=- -9580 deg-cm2dmol 1 for the poly (Pro)II component and —5560 deg-cm2-dmol 1 for the unordered component. These values provide a method for roughly estimating the poly(Pro)II content, /Pn, of an unordered peptide from [0]222 ... 

In Section 7.7.3.3, methods for quantitating a-helix and other secondary structural types in peptides were described. These are generally applicable to a series of peptides in which a regular conformation [a-helix, (3-sheet, poly(Pro)II] is in equilibrium with an ensemble of unordered conformations, as evidenced by an isodichroic point observed over a range of temperature, pH, or solvent composition. 

A protein molecule has the same conformation whenever it exists under the same conditions, and protein molecules with the same sequence of amino acids have identical conformations under identical conditions (Flory 1969 Mangino 1984). Some structures in protein chains are seen frequently in a variety of proteins and have been given names such as a-helix and 0-sheet. Others, referred to as unordered structure (Swaisgood 1982), are regions of protein folding which may be found only once, but are structurally stable. Much space in globular proteins is filled with such unordered structure (Flory 1969). 

The nucleation of parallel (3-sheet structure via metal ion chelation in aqueous solution was investigated by incorporating an ethylene glycol spacer between a dibenzofuran-4,6-dipro-panoic acid template and the two peptide strands (Scheme 6).[7 The flexibility of the ethylene glycol spacer allows the peptide to sample a variety of largely unordered conformations in the absence of metal ions. Upon binding of palladium(II), nickel(II), or copper(II) ions, the peptidomimetic adopts a well-defined (3-sheet conformation as discerned from biophysical and spectroscopic studies (i.e., CD, IR absorption, and H NMR spectrometry).17 The synthesis of the dibenzofuran-4,6-dipropanoic acid template was discussed... 

Novel properties of peptides can be obtained by incorporation of Saa. Peptides are characteristically highly flexible molecules whose 3D structure is strongly influenced by their environment. Their often unordered conformation in solution complicates their use in determining the receptor bound bioactive structure.182,831 Conformational constraints,184-881 cyclization/891 and/or replacement of the peptide backbone or parts of it162 90-921 can provide information on the required conformation for biological activity. 

S S CONTENTS Preface, C. Allen Bush. Methods in Macromo-lecular Crystallography, Andrew J. Howard and Thomas L. Poulos. Circular Dichroism and Conformation of Unordered Polypeptides, Robert W. Woody. Luminescence Studies with Horse Liver Dehydrogenase Information on the Structure, Dynamics, Transitions and Interactions of this Enzyme, Maurice R. Eftink. Surface-Enhanced Resonance Raman Scattering (SERRS) Spectroscopy A Probe of Biomolecular Structure and Bonding at Surfaces, Therese M. Cotton, Jae-Ho Kim and Randall E. Holt. Three-Dimensional Conformations of Complex Carbohydrates, C. Allen Bush and Perse-veranda Cagas. Index. 

CD analysis of recombinant human tropoelastin shows that the molecule is composed of 3% a-helix, 41% /3-sheet, 21% /3-turn, and 33% other structure (Vrhovski et al., 1997). FT-Raman studies on human elastin demonstrate derived secondary structures containing 8% a-helix, 36% /3-strand, and 56% unordered conformation (Debelle et al., 1998). 

Ma, K., and Wang, K. (2003). Malleable conformation of the elastic PEVK segment of titin Non-cooperative interconversion of polyproline II helix, beta-turn and unordered structures. Biochem.J. 374, 687-695. 

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