Alpha -helix

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 secondary stmcture of the plasminogen molecule, as determined by circular dichroism spectra, is 80% random coil, 20% beta-stmcture, and 0% alpha-helix. Electron microscopy has demonstrated the tertiary stmcture of plasminogen to be a 22- to 24-nm long spiral filament with a diameter of 2.2 to 2.4 nm. 

The helices at the N-terminal regions of the two polypeptide chains are intertwined and make extensive contacts in the central part of the molecule to form a stable core. This core supports two "heads", each comprising the last three helices from one polypeptide chain. Alpha helix 3 in the middle of the subunit chain is quite long and forms the main link between the core and the head. 

Figure 8.19 The a helices of the N-terminal region of the trp repressor are involved in subunit interactions and form a stable core in the middle of the dimer. Alpha helices 4-6, which include the helix-turn-helix motif, form two "head" regions at the two ends of the molecule. Alpha helix 3 connects the core to the head in both subunits. (Adapted from R.W. Schevitz et al., Nature 317 782-786, 1985.)...

FIGURE 6.24 (a) The alpha helix consisting of residues 153-166 (red) in flavodoxin from Anahaena is a surface helix and is amphipathic. (b) The two helices (yellow and blue) in the interior of the citrate synthase dimer (residues 260-270 in each monomer) are mostly hydrophobic, (c) The exposed helix (residues 74-87—red) of calmodulin is entirely accessible to solvent and consists mainly of polar and charged residues. 

Alpha farnesene, structure of, 207 Alpha helix (protein), 1038 Alpha-keratin, molecular model of, 1039... 

FIGURE F.l The research vessel Alpha Helix is used by chemists at the University of Illinois at Urbana-Champaign to search for marine organisms that contain compounds of medicinal value. Compounds found to have antifungal or antiviral properties are then subjected to the kinds of analvses described in this section. 

Johansson, J., Szyperski, T, Curstedt, T., and Wuthrich, K. The NMR structure of the pulmonary surfactant-associated polypeptide SP-C in an apolar solvent contains a valyl-rich alpha-helix. Biochemistry 1994, 33, 6015-6023. 

My interest at that time revolved around evaluating optical rotary dispersion data [12]. The paired values of optical rotation vs. wavelength were used to fit a function called the Drude equation (later modified to the Moffitt equation for William Moffitt [Harvard University] who developed the theory) [13]. The coefficients of the evaluated equation were shown to be related to a significant ultraviolet absorption band of a protein and to the amount of alpha-helix conformation existing in the solution of it. 

Segrest MP et al The amphipathic alpha-helix A multifunctional structural motif in plasma lipoproteins. Adv Protein Chem... 

The essential distinction between the approaches used to formulate and evaluate proteins, compared with conventional low molecular weight drugs, lies in the need to maintain several levels of protein structure and the unique chemical and physical properties that these higher-order structures convey. Proteins are condensation polymers of amino acids, joined by peptide bonds. The levels of protein architecture are typically described in terms of the four orders of structure [23,24] depicted in Fig. 2. The primary structure refers to the sequence of amino acids and the location of any disulfide bonds. Secondary structure is derived from the steric relations of amino acid residues that are close to one another. The alpha-helix and beta-pleated sheet are examples of periodic secondary structure. Tertiary... 

Harper, S. M., J. M. Christie, and K. H. Gardner (2004). Disruption of the LOV-J alpha helix interaction activates phototropin kinase activity. Biochemistry 43 16184-16192. 

Sitkoff D, Lockhart DJ, Sharp KA, Honig B (1994) Calculation of electrostatic effects at the amino terminus of an alpha helix. Biophys J 67 2251-2260... 

Taylor, J.W., N.J. Greenfield, B. Wu, and P.L. Privalov. 1999. A calorimetric study of the folding-unfolding of an alpha-helix with covalently closed N- and C-terminal loops. J Mol Biol 291 965-976. 

The Alpha Helix Expedition to the Amazon for the Study of Fish Bloods and Hemoglobins. Comp. Biochem. Physiol. 624 (1) (1979). 

A synthetic peptide has been designed to mimic the effects of viral fusogenic properties (114,115). It consists of 30 amino acids with the major repeat of Glu-Ala-Leu-Ala so, it is referred to as a GALA peptide. It undergoes a conversion from an aperiodic conformation at neutral pH and becomes an amphipathic alpha helix at pH 5. In the more acidic environment, the peptide interacts with lipid bilayers (114,115). GALA has been incorporated into transferrin-targeted liposome, with the effect of significantly... 

Concerning the helical stmcture of biological macromolecules in general, they relied on Linus Pauling s discovery of the alpha-helix stmcture of proteins and concerning the helical stmcture of DNA, they relied on Rosalind Franklin s X-ray diffraction pattern of DNA. 

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