Conformational fluctuations peptide

To describe correlated peptide conformation fluctuations in internal coordinates, the multivariate Gaussian distribution fiG used for characteristic packets and integration kernels in Cartesian space must be adapted to the periodic and multiply connected torsion angle space. Although the Carte-... 

Section 7.3.1 describes the experimental apparatus for collecting and analyzing fluorescence lifetime data vs temperature. Section 7.3.2 presents the results of lifetime measurements of polyproline peptides and MD simulations to (a) relate fluorescence quenching rates to specific conformational fluctuations, and (b) calculate the implications of intramolecular electrostatic interactions for the quenching mechanism. 

S. Kimura, A. Naito, S. Tuzi, H. Saito, A C NMR Study on [3- C]-, [1- CjAlaor [l- C]Val-kbeled Transmembrane Peptides of bacteriorhodopsin in hpid bilayers insertion, rigid-body motions and local conformational fluctuations at ambient temperature, Biopolymers 58 (2001) 78-88. 

The free energy differences obtained from our constrained simulations refer to strictly specified states, defined by single points in the 14-dimensional dihedral space. Standard concepts of a molecular conformation include some region, or volume in that space, explored by thermal fluctuations around a transient equilibrium structure. To obtain the free energy differences between conformers of the unconstrained peptide, a correction for the thermodynamic state is needed. The volume of explored conformational space may be estimated from the covariance matrix of the coordinates of interest, = ((Ci [13, lOj. For each of the four selected conform-... 

It is emphasized that revealing the dynamics as well as the structure (or conformation) based on several types of spin-relaxation times is undoubtedly a unique and indispensable means, only available from NMR techniques at ambient temperature of physiological significance. Usually, the structure data themselves are available also from X-ray diffraction studies in a more refined manner. Indeed, better structural data can be obtained at lower temperature by preventing the unnecessary molecular fluctuations, which are major subjects in this chapter, since structural data can be seriously deteriorated for domains where dynamics are predominant even in the 2D or 3D crystalline state or proteoliposome at ambient temperature. It should be also taken into account that the solubilization of membrane proteins in detergents is an alternative means to study structure in solution NMR. However, it is not always able faithfully to mimick the biomembrane environment, because the interface structure is not always the same between the bilayer and detergent system. This typically occurs in the case of PLC-81(1-140) described in Section 4.2.4 and other types of peptide systems. 

We now turn to several examples where these techniques have been applied to peptide hormones, and show how we can study the conformational properties, including conformational minima and fluctuations, dynamics, and energetics of these molecules, and how these properties can in turn be used to design analogs. 

We have been more concerned with the nature of the water around proteins and peptides. To this end we have investigated the structure and energetics of the solvent, both ordered and disordered around the enzyme lysozyme, in the triclinic crystal[l7d]. In addition to lysozyme, we have characterized the water structure and fluctuations in the crystal of a cyclic hexapeptide, (L-Ala-L-Pro-D-Phe)9[20]. and studied the effect of solvent on the conformation of the dipeptide of alanine[2l] and on the equilibria between extended and helical alanine polypeptides such as those discussed in the previous section[22]. The latter systems simulate aqueous solution conditions rather than crystalline environment. 

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