Protein neighbor

One way in which to probe the structural surroundings of a protein is to monitor the pH behavior of specific carbon sites of the C probes. pH-titration studies, of given resonances, had previously been used for probing of the protein structure, because they are known to provide information concerning electrostatic (salt-bridging) interactions in the protein, neighboring group-ionizations, and local environments. ... 

Neighbor joining Neighbor DNA/Protein Neighbor joining analysis... 

Dontsova, O.A., Rosen, K.V., Bogdanova, S.L., Skripkin, E.A., Kopylov, A.M. and Bogdanov, A.A. (1992). Identification of the Escherichia coli 30S ribosomal subunit protein neighboring mRNA during initiation of translation. Biochimie 74, 363-371. 

Figure 7.10. The protein neighbor for the M. thermoautotrophicum tfx gene. Clicking on the Protein hyperlink next to the first entry in Figure 7.9 leads the user to this GenPept entry. See text for details.

Secondary structure (Section 27 19) The conformation with respect to nearest neighbor ammo acids m a peptide or pro tern The a helix and the pleated 3 sheet are examples of protein secondary structures... 

Because it is desirable to break a peptide this way, some flexibility is required in the rigorous definition of sp -sp single bond. In particular, the dative Cqj-N bond in the backbone of a peptide is considered to be such a bond since the definition is based on the number of neighbors — four for carbon, three for nitrogen, two for Oxygen, etc. If this were not the case, you couldn t break a protein into classical and quantum regions at all. 

Eor a macromolecule such as a large protein, the steps in characterization involve, first, identification of the spin systems present, using correlated spectroscopy, and identification of neighboring amino acids. The long range noes are then assigned, and three bond coupling constants ate deterrnined. 

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

The conformation an amino acid adopts depends on the residues in its neighborhood. This was made clear from a study of identical pentapeptides in unrelated proteins which were observed to adopt the same conformation only 20% of the time (24). The effect that residues neighboring in sequence or in space have on the conformation is not well understood. 

Coagulation Factors II, III, VII, IX, X, XI, and Xlla fragments, thrombin, and plasmin are classified as serine proteases because each possesses a serine residue with neighboring histidine and asparagine residues at its enzymatically active site (Table 3). Factors II, VII, IX, and X, Protein C, Protein S, and Protein Z are dependent on the presence of vitamin K [84-80-0] for their formation as biologically functionally active procoagulant glycoproteins. 

X-ray studies at 22.5 A resolution of murine polyomavlrus by 1. Rayment and D.L.D. Caspar at Brandeis University confirmed the presence of these 72 capsomers at the expected positions, but even at low resolution the pentagonal shape of all 72 capsomers was evident (Figure 16.22). They concluded that each capsomer must be a pentameric assembly of the major viral subunit, known as viral protein 1 (VPl). Each of the 60 icosahedral asymmetric units contains 6 VPl subunits, not 7, and the complete shell contains 360 VPl subunits. The 12 VPl pentamers centered on icosahedral fivefold axes are identically related to their five neighbors, but the 60 pentamers centered on pseudosixfold positions "see" each of their 6 neighbors quite differently (Figure 16.23). How can such diversity of interaction be incorporated into the bonding properties of just one type of protein subunit, without compromising specificity and accuracy of assembly ... 

The capsids of polyoma virus and the related SV40 have icosahedral symmetry, with 72 pentameric assemblies of the major capsid protein. The pentamers are linked to their neighbors by flexible arms, with a p strand that augments a p sheet in the invaded pentamer. These flexible arms allow the pentamers to be linked together with both fivefold and sixfold symmetry. 

Glycine residues have more conformational freedom than any other amino acid, as discussed in Chapter 1. A glycine residue at a specific position in a protein has usually only one conformation in a folded structure but can have many different conformations in different unfolded structures of the same protein and thereby contribute to the diversity of unfolded conformations. Proline residues, on the other hand, have less conformational freedom in unfolded structures than any other residue since the proline side chain is fixed by an extra covalent bond to the main chain. Another way to decrease the number of possible unfolded structures of a protein, and hence stabilize the native structure, is, therefore, to mutate glycine residues to any other residue and to increase the number of proline residues. Such mutations can only be made at positions that neither change the conformation of the main chain in the folded structure nor introduce unfavorable, or cause the loss of favorable, contacts with neighboring side chains. 

FIGURE 1.9 (a) Amino acids build proteins by connecting the n-carboxyl C atom of one amino acid to the n-amino N atom of the next amino acid in line, (b) Polysaccharides are built by combining the C-1 of one sugar to the C-4 O of the next sugar in the polymer, (c) Nucleic acids are polymers of nucleotides linked by bonds between the 3 -OH of the ribose ring of one nucleotide to the 5 -P04 of its neighboring nucleotide. All three of these polymerization processes involve bond formations accompanied by the elimination of water (dehydration synthesis reactions). 

AQPO, formerly known as the Major Intrinsic Protein of 26 kDa (MDP26), is specifically expressed in the plasma membrane of eye lens fiber cells. It transports water to a low degree, but has also been implicated in cell adhesion and gap junction formation. Its main role is to maintain the transparency of the lens by maintaining a tight cellular connection to neighboring cells and/or by controlling the fluid circulation. 

Proteins may also Have a quaternary structure, in which neighboring polypeptide units stack together in a specific arrangement. The hemoglobin molecule, for example, has a quaternary structure of four polypeptide units, one of which is shown in Fig. 19.20. 

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