Helix motions

For proteins with significant helical content it is possible to show that larger-scale displacements involve rigid-body motions of the helices. Two such proteins for which molecular dynamics simulations have been analyzed in terms of helix motions are the C-terminal fragment of the L7/L12 ribosomal protein of E. coli229 and myoglobin.230 

The C-terminal fragment of L7/L12 consists of 68 amino acids and is composed of a layer containing three antiparallel a-helices over a twisted antiparallel /3-sheet with a connectivity. A 150-ps vacuum simulation229 

The adiabatic mapping technique used in the lysozyme study has now been 

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Are the helical movements detected by the spin labels functionally important If so, a molecular cross-link between the helix in question and an adjacent helix that does not move or moves in a different direction should block activation of transducin. To implement this strategy to identify functionally relevant helix motions, two different kinds of interhelical cross-links have been employed. In the first, helices are cross-linked by spontaneous or catalyzed disulfide formation between two cysteines, one engineered in each helix. In the second, cross-links are introduced by binding of Zn2+ to engineered histidine ligands, one in each helix (Elling et al., 1995). 

The pattern of helix motions observed experimentally suggests a simple model for the activated state in which helices on opposite sides of the chromophore binding pocket move outward to open a cleft in the molecule (Fig. 20). In the prose of Henry Bourne, the molecule has blossomed (Meng and Bourne, 2001) to expose new surfaces for coupling of rhodopsin with transducin. 

Example Molecular dynamics simulations of selected portions of proteins can demonstrate the motion of an amino acid sequence while fixing the terminal residues. These simulations can probe the motion of an alpha helix, keeping the ends restrained, as occurs n atiirally m transmembrane proteins. You can also investigate the conformations of loops with fixed endpoints. 

The furanose rings of the deoxyribose units of DNA are conformationally labile. All flexible forms of cyclopentane and related rings are of nearly constant strain and pseudorotations take place by a fast wave-like motion around the ring The flexibility of the furanose rings (M, Levitt, 1978) is presumably responsible for the partial unraveling of the DNA double helix in biological processes. 

Resonance Raman Spectroscopy. If the excitation wavelength is chosen to correspond to an absorption maximum of the species being studied, a 10 —10 enhancement of the Raman scatter of the chromophore is observed. This effect is called resonance enhancement or resonance Raman (RR) spectroscopy. There are several mechanisms to explain this phenomenon, the most common of which is Franck-Condon enhancement. In this case, a band intensity is enhanced if some component of the vibrational motion is along one of the directions in which the molecule expands in the electronic excited state. The intensity is roughly proportional to the distortion of the molecule along this axis. RR spectroscopy has been an important biochemical tool, and it may have industrial uses in some areas of pigment chemistry. Two biological appHcations include the deterrnination of helix transitions of deoxyribonucleic acid (DNA) (18), and the elucidation of several peptide stmctures (19). A review of topics in this area has been pubHshed (20). 

The presence of a static magnetic field within a plasma affects microscopic particle motions and microscopic wave motions. The charged particles execute cyclotron motion and their trajectories are altered into heUces along the field lines. The radius of the helix, or the T,arm or radius, is given by the following ... 

An important characteristic of biomolecular motion is that the different types of motion are interdependent and coupled to one another. For example, a large-scale dynamic transition cannot occur without involving several medium-scale motions, such as helix rearrangements. Medium-scale motions cannot occur without involving small-scale motions, such as side-chain movement. Finally, even side-chain motions cannot occur without the presence of the very fast atomic fluctuations, which can be viewed as the lubricant that enables the whole molecular construction to move. From the point of view of dynamic... 

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