Alpha-helical proteins

Cohen, C., and Parry, D. A. D. (1990). Alpha-helical coiled coils and bundles - how to design an alpha-helical protein. Proteins 7, 1-15. 

Hardin, C., et ah, Associative memory hamiltonians for structure prediction without homology alpha-helical proteins. Proc Natl Acad Sci USA, 2000. 97(26) p. 14235-40. 

P. C, Weber and F. R. Salemme, Nature (London), 287, 82 (1982), Structural and Functional Diversity in 4-Alpha-Helical Proteins,... 

Figure 7 A hypothetical pathway by which an all beta sheet protein (a) might evolve into an all alpha-helical protein (h) by a series of insertions and deletions. Beta sheets are designated by lower case letters and alpha helices by upper case letters. Red arrows indicate a clear evolutionary relationship, orange arrows indicate a possible evolutionary relationship, and black arrows indicate no evolutionary relationship, (a) C-terminal domain of Bacillus licheniformis a-amylase (1BPL) ...

Zagrovic, B., Snow, C.D., Shirts, M.R., Pande, V.S. Simulation of folding of a small alpha-helical protein in atomistic detail using worldwide-distributed computing. J. Mol. Biol. 2002, 323(5), 927-37, November. 

A modified version of this procedure has been described by Wolfram and MiUigan [118]. Their procedure involves esterificahon of the carboxyl groups that are beheved to reside primarily on the alpha-helical proteins and proteins of the hair surface. Esterificahon decreases the solubility of these proteins, allowing the nonesterified proteins (of the matrix) to be extracted more easily. The soluble fraction of this procedure is called gamma -keratose it resembles gamma-keratose but provides a higher yield. The insoluble residue exhibits birefringence and is called the alpha-beta -keratose fraction. 

Ackbarow T, Sen D, Thaulow C, Buehler MJ (2009) Alpha-helical protein networks are self-protective and flaw-tolerant. PLoS One 4(6) e6015... 

The idea that solitons might play an important role in biopolymers comes from Davydov. In his article [37], he studied alpha-helical proteins and applied some achievements of nonlinear mathematics to biology. As for DNA, the nonlinear physics started in 1980 [10] when the first nonlinear Hamiltonian of DNA, as well as possibility of sohtonic solution, was suggested. A crucial experimental research was explained in Ref. [38], representing victory of nonlinear over linear DNA physics. 

Alpha helices in proteins are found when a stretch of consecutive residues all have the 0, y angle pair approximately -60° and -50°, corresponding to the allowed region in the bottom left quadrant of the... 

Figure 2.2 The a helix is one of the major elements of secondary structure in proteins. Main-chain N and O atoms ate hydrogen-bonded to each other within a helices, (a) Idealized diagram of the path of the main chain in an a helix. Alpha helices are frequently illustrated in this way. There are 3.6 residues per turn in an a helix, which corresponds to 5.4 A (1.5 A pet residue), (b) The same as (a) but with approximate positions for main-chain atoms and hydrogen bonds Included. The arrow denotes the direction from the N-terminus to the C-termlnus.

Alpha helices that cross membranes are in a hydrophobic environment. Therefore, most of their side chains are hydrophobic. Long regions of hydrophobic residues in the amino acid sequence of a protein that is membrane-bound can therefore be predicted with a high degree of confidence to be transmembrane helices, as will be discussed in Chapter 12. 

Alpha helices are sufficiently versatile to produce many very different classes of structures. In membrane-bound proteins, the regions inside the membranes are frequently a helices whose surfaces are covered by hydrophobic side chains suitable for the hydrophobic environment inside the membranes. Membrane-bound proteins are described in Chapter 12. Alpha helices are also frequently used to produce structural and motile proteins with various different properties and functions. These can be typical fibrous proteins such as keratin, which is present in skin, hair, and feathers, or parts of the cellular machinery such as fibrinogen or the muscle proteins myosin and dystrophin. These a-helical proteins will be discussed in Chapter 14. 

Cohen, C., Parry, D.A.D. Alpha-helical coiled coils—a widespread motif in proteins. Trends Biochem. Sci. 

Figure 12.1 Four different ways in which protein molecules may be bound to a membrane. Membrane-bound regions are green and regions outside the membrane are red. Alpha-helices are drawn as cylinders and P strands as arrows. From left to right are (a) a protein whose polypeptide chain traverses the membrane once as an a helix, (b) a protein that forms several transmembrane a helices connected by hydrophilic loop regions,...

Alpha helices D and E from the L and M subunits (Figure 12.14) form the core of the membrane-spanning part of the complex. These four helices are tightly packed against each other in a way quite similar to the four-helix bundle motif in water-soluble proteins. Each of these four helices provides a histidine side chain as ligand to the Ee atom, which is located between the helices close to the cytoplasm. The role of the Ee atom is probably to... 

FIGURE 21.11 The structure of UQ-cyt c reductase, also known as the cytochrome hci complex. The alpha helices of cytochrome b (pale green) define the transmembrane domain of the protein. The bottom of the structure as shown extends approximately 75 A into the mitochondrial matrix, and die top of the structure as shown extends about 38 A into the intermembrane space. (Photograph kindly provided by Di Xia and Johann Deismhofer [From Xia, D., Yn, C.-A., Kim, H., Xia,J-Z., Kachnrin, A. M., Zhang, L., Yn,... 

Fig. 4.1.13 A ribbon representation of the crystal structure of recombinant acquorin molecule showing the secondary structure elements in the protein. Alpha-helices are denoted in cyan, beta-sheet in yellow, loops in magenta coelenterazine (yellow) and the side chain of tyrosine 184 are shown as stick representations. From Head et al., 2000, with permission from Macmillan Publishers.

A leucine zipper is a structural motif present in a large class of transcription factors. These dimeric proteins contain two extended alpha helices that grip the DNA molecule much like a pair of scissors at adjacent major grooves. The coiled-coil dimerization domain contains precisely spaced leucine residues which are required for the interaction of the two monomers. Some DNA-binding proteins with this general motif contain other hydrophobic amino acids in these positions hence, this structural motif is generally called a basic zipper. 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Dey S., Alpha Helical Peptide Nucleic Acids (Alpha PNAs) - Integration of Protein Structure and Nucleic Acid Function. PhD thesis. Case Western Reserve University, Cleveland, OH, January 2001. 

The N-terminal domain of the OCP is an orthogonal alpha-helical bundle, subdivided into two four-helix bundles (Figure 1.3a and c). These subdomains are composed of discontinuous segments of the polypeptide chain (gray and white in Figure 1.3c). To date, the OCP N-terminal domain is the only known protein structure with this particular fold (Pfam 09150). The hydroxyl terminus of the 3 -hydroxyechinenone is nestled between the two bundles. The C-terminal domain (dark... 

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