Alpha helix terminus

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... 

Complete the following structure to form a short segment of alpha helix. Extend the chain by at least three residues. Form all hydrogen bonds correctly Add at least three side chains with the correct chirality at the alpha carbon positions. Add one electrically charged side chain and show how it interacts with the peptide backbone at either the C- or N-terminus to help stabilize the helix. 

Choose chain conformation (Alpha Helix or Beta Sheet or Other) and isomer (l or d), and pick amino acids from the N-terminus. 

For polypeptide, the B program provides options for building various protein conformations including 3-10 helix, alpha helix, alpha helix (L-H), beta sheet (anti-prl), beta sheet (parallel), various beta turns, extended, gamma turns, omega helix, pi helix, polyglycine, and polyproline. Choose the desired conformation and isomer (l or d) and then add amino acids from N-terminus to construct polypeptide chain. 

Lockhart, D. J. and P. S. Kim. (1992). Internal stark effect measurement of the electric field at the amino terminus of an alpha helix. Science. 257 947-51. 

The linear peptide as observed in its primary structure starts folding on itself because of the interactions among the side chains of the adjacent amino acids. This leads to the formation of different structures, which include (a) helical structure called an alpha helix, (b) stranded folds called beta sheets or beta strands, and (c) random coils. Now, certain criteria can be used to predict the occurrence of these structures in the secondary structure of the protein. This was first established by Chow and Fasman (1978) based on the propensity of certain amino acids associated with these structures, i.e., helix and beta sheet. For example, the amino acids glu, met, ala, and lys are predominantly associated with the helix structure whereas the amino acids val, ile, and tyr are strongly associated with the beta sheet structure. The amino acid leucine is associated with both the helix and the beta sheet. The amino acids glycine and proline occur as breakers of the helix proline usually occurs as the first residue in the helix. Also, asp and glu occurs at the N-terminus, whereas arg and lys occur at the C-terminus. 

Dialkylglycine decarboxylase (DGD) is unusual as it catalyzes both a decarboxylation and a transamination during its normal catalytic cycle. DGD uses stereoelectronic effects to control its unusual reaction specificity. The three-dimensional structure of DGD showed that the enzyme possesses two binding sites for monovalent cations (MVCs). In particular, one site, located near the active site, hinds potassium ions and controls the catalytic activity. The other is located at the carboxyl terminus of an alpha helix and prohahly has a structural role. 

The active site of type 3 copper proteins consists of two copper atoms. Each of them is bound by three histidines provided by an antiparallel alpha-helix pair (Figure 1). Cu-A denotes the copper-binding site closer to the N-terminus, whereas Cu-B is the copper-binding site closer to the C-terminus. According to crystal structures of arthropod and mollusc hemocyanins, the coppers bind a dioxygen molecule in the same way as a peroxide in side-on... 

Beta sheet. The beta sheet involves H-bonding between backbone residues in adjacent chains. In the beta sheet, a single chain forms H-bonds with its neighboring chains, with the donor (amide) and acceptor (carbonyl) atoms pointing sideways rather than along the chain, as in the alpha helix. Beta sheets can be either parallel, where the chains point in the same direction when represented in the amino- to carboxyl- terminus, or antiparallel, where the amino- to carboxyl- directions of the adjacent chains point in the same direction. (See Figure 5-5.)... 

In a recent theoretical study, Shipman (36) proposed several specific models for the herbicide binding site on PS II. It was proposed that the PS II herbicides bind electrostatically at or near a protein salt bridge or the terminus of an alpha helix. 

Willey et al. (1) have monitored carboxypeptidase digestion of cytochrome f (Cyt f) in intact thylakoid membranes. They have presented a model of the orientation of Cyt f in the thylakoid membrane where residues 251-270 form a transmembrane alpha-helix, residues 271-285 are in the stroma and the remainder of the molecule resides in the intra-thylakoid space. It has been postulated that the solubility of purified Cyt f, from members of the Cruciferae, is due to the loss of the transmembrane alpha-helix during purification. Turnip Cyt f is soluble and, upon electrophoresis in the presence of SDS (SDS-PAGE), is resolved into diffuse double bands with Mp of 28 and 32 Kd. The predicted Mp of sequenced cytochromes f is 31 Kd and a loss of 4 Kd from tne C-terminus would include all of the presumed membrane spanning alpha-helix. The remaining Cyt f would be more negative by 2 units. 

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.

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... 

A) The protein coat of horse spleen apoferritin deduced from x-ray diffraction of crystals of the protein.The outer surface of the protein coat shows the arrangement of the 24 ellipsoidal polypeptide subunits. N refers to the N-terminus of each polypeptide and E to the E-helix (see B). Note the channels that form at the four-fold axes where the E-helices interact, and at the threefold axes near the N-termini of the subunits. (B) A ribbon model of a subunit showing the packing of the four main alpha-helices (A, B, C, and D), the connecting L-loop and the E-helix. 

Figure 29-9 Selected views of aminoacyl-tRNA sjmthetase stmcture and action. (A) Alpha-carbon trace of the type IE. coli glutaminyl-tRNA synthetase. The phosphate backbone of tRNA " is shown in black ATP is shown in the active-site cleft. The canonical dinucleotide fold domain near the N terminus is shaded. Two structural motifs (black), proposed to link the active site with regions of the protein-RNA interface involved in tRNA discrimination, are indicated. The a helix (top) connects tRNA recognition in the minor groove of the acceptor stem with binding of the ribose group of ATP. The large loop (center) connects anticodon recognition by the two P-barrel domains (bottom) with sequences flanking the MSK sequence motif, which interacts with the phosphates of ATP. From Perona et Courtesy of Thomas A. Steitz. (B) The active site...

The structure of the kinesin monomer is classified into the three subdomains—head, neck-linker, and tail (see Figure I.IA). The head domain (residue 1-323) contains a nucleotide-binding pocket, a catalytic site, which controls the conformational state of the neck-linker (residue 324-338) made of 15 amino acids. The neck-helix domain (residues from 339 to the C-terminus), extended from the neck-linker, forms an alpha-helical structure dimeric kinesins are made via coiled-coil interactions between the neck-helices from two monomers (see Figure I.IA). 

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