Amino acid residue assignment

This section briefly reviews prediction of the native structure of a protein from its sequence of amino acid residues alone. These methods can be contrasted to the threading methods for fold assignment [Section II.A] [39-47,147], which detect remote relationships between sequences and folds of known structure, and to comparative modeling methods discussed in this review, which build a complete all-atom 3D model based on a related known structure. The methods for ab initio prediction include those that focus on the broad physical principles of the folding process [148-152] and the methods that focus on predicting the actual native structures of specific proteins [44,153,154,240]. The former frequently rely on extremely simplified generic models of proteins, generally do not aim to predict native structures of specific proteins, and are not reviewed here. 

Peptide is the name assigned to short polymers of amino acids. Peptides are classified by the number of amino acid units in the chain. Each unit is called an amino acid residue, the word residue denoting what is left after the release of HgO when an amino acid forms a peptide link upon joining the peptide chain. Dipeptides have two amino acid residues, tripeptides have three, tetrapeptides four, and so on. After about 12 residues, this terminology becomes cumbersome, so peptide chains of more than 12 and less than about 20 amino acid residues are usually referred to as oligopeptides, and, when the chain exceeds several dozen amino acids in length, the term polypeptide is used. The distinctions in this terminology are not precise. 

Fig. 2 Chemical shift perturbation and chemical shift mapping, (a) Portions of the [15N, 1H]-HSQC spectra of Bcf-xL recorded in absence (black) and in presence of each of the four molecules (in colors). Resonance assignments for amino acid residues that exhibit large shifts are reported, (b) Structure of Bc1-Xl in complex with the BH3 peptide from Bak (PDB code 1BXL) showing the chemical shift changes in Bcl-xL upon ligand binding (blue, large shits yellow, no shifts the Bak peptide is reported in cyan). Adapted from [48]...

On the other hand, resonance assignments for CP of threonine and serine, and C and Cy of hydroxy proline, were difficult to make, because of their proximity to carbohydrate carbon resonances. In most cases then, the resonances were assigned on the basis of the effects of pH on the chemical shifts of those resonances. It was shown that the chemical shifts for the carbohydrate carbon resonances were virtually unaffected (AS 0.4 p.p.m.) when going from the cationic state (pH 2) to the anionic state (pH 11) of the amino acid residues. The chemical shifts of C and CP of the amino acid residues, however, shifted considerably (up to 3.1 and 6.6 p.p.m. for C" and CP, respectively see Table VI). 

Physical-chemical characteristics of prion proteins are evident after assigning different parameters, including hydrophobicity, charge, and molecular weight to the amino acid residues (Inouye and Kirschner, 1991, 1998) (Table II, Fig. 5). The sequences among different animals... 

More recently, homonuclear correlation techniques relying on J-couplings have also been developed [86, 87, 89] and applied to the assignment of spin systems of amino-acid residues in uniformly labeled proteins and peptides [90]. These have, in some cases, a higher information content than the comparable dipolar-mediated experiments, as relayed correlations throughout the continuous 13C-13C network are more easily realized at high B0 fields [90]. 

In the absence of crystallographic or NMR data, predictive techniques based on protein primary sequences can be used to elaborate crude 3D models. Such models will suggest that certain amino acid residues are involved in forming the active (receptor) site. The assignment of structural or functional roles to particular residues can be tested by site-directed mutagenesis, and the model can be further refined by consideration of SAR among ligands. 

Matrix schemes which assign end effects to each end of a helical segment are also proposed. A 3 x3 statistical weight matrix B using this weighting scheme is used here. Row index states of amino acid residues i-1 and /, while columns index states of amino acid residues i and /+ 1. 

Exactly how the amino acid sequence determines three-dimensional structure is not understood in detail, nor can we always predict function from sequence. However, protein families that have some shared structural or functional features can be readily identified on the basis of amino acid sequence similarities. Individual proteins are assigned to families based on the degree of similarity in amino acid sequence. Members of a family are usually identical across 25% or more of their sequences, and proteins in these families generally share at least some structural and functional characteristics. Some families are defined, however, by identities involving only a few amino acid residues that are critical... 

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