Secondary structure assignmentbottom - . CUBIC- papers - . Rost group. Secondary structure assignment. Claus A Andersen 1,* &. Burkhard Rost 2,3,4. Siena Biotech Spa. Via Fiorentina 1, 5. Siena, Italy. 2Dept. Nicholas Avenue Rm 8. New York, NY 1. 00. USA4. North East Structural Genomics Consortium (NESG), Columbia University, 1. St. Nicholas Avenue Rm 8. New York, NY 1. 00. USA5. New York Consortium On Membrane Protein Structure (NYCOMPS), Columbia University, 1. St. Nicholas Avenue Rm 8. New York, NY 1. 00. USA*Corresponding author: Claus Andersen via: admin@rostlab. URL http: //www. rostlab. We provide a comprehensive review of methods used to assign. This. is a much revised second edition of a previously published review. When looking at how chains of amino acids in proteins are. D structure of practically all. Chapter 2). These structures were. Linderstr. There is. D coordinates. Instead there are many different assignment. H- bonds and van. Waals), geometrical idealization (e. G refers to 3. 10- helix. DSSP; classes are the groups. G, H and I all describing helices in DSSP; regular. Note that non- regular. Super. secondary structure refers to the relative spatial distances and orientations. Secondary-structure prediction. PSSpred A multiple neural network training program for protein secondary structure. A java based protein secondary structure prediction program on. STRIDE for protein secondary structure assignment. Protein structure prediction is the inference of. Secondary structure prediction is a set of. STRIDE) applied to the crystal structure of. A protein structure prediction program using. SABLE and SPINE-X for protein secondary structure prediction were. Prediction of structural features and application to. Protein Secondary Structure Prediction Servers and. Improvements in Protein Secondary Structure Prediction by an Enhanced. Program, NNSSP (Salamov. Initioā€¯ secondary structure prediction. Modeller is a program you download. NNPREDICT Protein Secondary Structure Prediction: A program that. PREDATOR Secondary structure prediction from. STRIDE: Protein secondary structure. Usage of secondary structure. The application of secondary. Chapter. 9) and the related task of structure comparison and classification (see. Chapters 1. 6,1. 7, and 1. Secondary structure has also been employed in protein. Chapter 2. 9), as well as in studies of. The one- dimensional. Some applications will be treated in more detail below. History: from expert to automatic assignment of. Pauling. and colleagues correctly predicted the idealized protein secondary structures. Pauling, Corey, and. Branson, 1. 95. 1), p- helices (Pauling. Corey and Branson, 1. Pauling and Corey, 1. Five decades. later, we know that on average about half of the residues in proteins. Berman et al., 2. Pauling and colleagues. Andersen, 2. 00. 1). Initially, the. crystallographers assigned secondary structure by eye from the 3. D structures. However, it. This was particularly. Kabsch & Sander to automate the assignment in their. DSSP program (1. 98. Originally developed to improve secondary. DSSP has remained the standard in the field, most popular. Curiously, the prediction method for. Kabsch & Sander originally needed the automatic assignment was never. Experimental investigations of protein secondary. X- ray crystallography (see Chapter 4) is widely used and generally provides. NMR (see Chapter 5). Doerr, 2. 00. 7). Optical spectroscopy is a much faster. H- bond dynamics at a picosecond time. Kolano, 2. 00. 6). In particular circular dichroism (CD) and Raman spectroscopy. X- ray data (Lees, 2. Tetin, 2. 00. 3. Janes, 2. This allows the rapid assessment of conformational changes resulting. Spectroscopy. resolution can be further enhanced with residue- specific isotope labeling e. Using the hydrogen bond spurs from the notion of. Following this notion the. Waals interaction. Likewise mathematical concepts are applied to secondary. These may be basic geometrical objects which can be. The rich network of hydrogen bonds in water creates a. This results in. missing water- water hydrogen bonds and therefore a relative energy cost. Isoleucine and Leucine when. Glycine (Creighton, 1. This energy cost is in the order of two. The packing of non- polar residues in the core is believed to. Hvidt and Westh, 1. Packing the non- polar residues in the core also means. To avoid this heavy energetic cost, the polarities are paired (forming. If. instead the protein backbone were non- polar, the protein core elements would. Approximately 9. 0% of the backbone C=O and NH groups. Baker and Hubbard, 1. Using the Coulomb. C=O and NH groups participate in intra- backbone hydrogen bonds. Andersen, 2. 00. 1). Pauling defined secondary structure by the intra- backbone. Thus, for simplicity, we refer to intra- backbone hydrogen. There are many different angles and distances that can be. Baker and Hubbard (1. NHO = q and distance. HO in the hydrogen bond. A hydrogen bond is assigned when: q > 1. Although a rather. One way of finding hydrogen bonds is by calculating the. Coulomb energy in the bond, as applied in DSSP (see below) focusing on the. Fig. The Coulomb energy for the attraction and. A cut- off level has been set for the weakest acceptable hydrogen bond so that the resulting energy is bound by: E < - 0. DSSP. In practice, the hydrogen atom position is usually not given in PDB files requiring an extrapolation. For example, the hydrogen atom position that is needed to calculate the two distances r. OH and r. HC' in eqn. PDB files. DSSP circumvents this problem by using an approximate position, assuming that the covalent bond between O=C' is parallel to the covalent N- H bond adjacent to the same polypeptide bond. The direction of the O=C' vector is kept while its length is set to 1 . The position of the H- atom is extrapolated using the direction of the C'=O vector when starting out from the position of the N- atom. These approximations made by DSSP simplify the calculation of the H- atom position and appear to be rather accurate despite the assumptions that were being made. When compared to the original bond angles and distances (Chreighton, 1. DSSP approximation to yield an average error around 0. The assumption of the trans- peptide bond, giving rise to the rigid peptide plane, was used by DSSP as well as our tests. Partitioning ab initio energy calculations of the hydrogen bond into classical components showed that about 7. Coulombic) and less than 5% comes from polarization and charge- transfer, for moderate strength bonds (Jeffrey and Saenger ,1. Note that the Coulomb energy term does not incorporate atom- atom repulsion to penalize steric clashes and does not give rise to a characteristic hydrogen bond length. Fig. 1: Distances used to calculate the Coulomb hydrogen bond energy. An empirical hydrogen bond energy calculation can be derived. Boobbyer, 1. 98. 9; Wade, 1. STRIDE (see below). The total energy Ehb depends on. NO distance energy Er, (reflecting optimal atom distance and. Ep. and Et (reflecting favorable hydrogen bond angles extrapolated from. The distance dependency energy Er is similar to the Lennard- Jones potential for the van der Waals interaction, but uses powers of 8 and 6 instead of 1. Thus reducing the slope of the atom- atom superposition term, whereby the penalty for superpositions is more lenient towards experimental inaccuracies in atom position determination. NO distance, rm is the optimal distance and Em, the optimal energy. For intra- backbone hydrogen bonds rm = 3. The two angular dependent terms are: where the angles q, ti and t. Fig. 2 : Angles and distances defining the empirical hydrogen bond. This energy evaluation is calculated for. EAij) and subsequently summed over all. ERij). EAij. has the same functional form as the Amber force field (Cornell, 1. EAij is the energy between atoms i and j with observed distance Rij . The optimal distance, mixing rules and polar charges where taken from Amber. In the special cases of Glycine and Proline, the backbone constellation has been adjusted accordingly by adding another Ha and removing the HN respectively. In b- spider the hydrogen atom positions were extrapolated geometrically from the N, Ca, C' and O coordinates using bond lengths, valence and torsion angles from Amber (Cornell, 1. This is very informative about. Vo. TAP (see below). Each Ca. is contained within a Vorono. This is a unique decomposition with non- overlapping cells that. Ca atom. each and where all internal space inside the protein is contained within a cell. Fig. A unique Ca atom contact map can thus be defined as the polyhedra sharing a contact surface. The example shown is Crambin (Teeter, 1. PDB: 1crn) visualized from an angle similar to the one employed in Fig. A, using the voro. D tool made available to the community by Frank Dupuis (Table 1). Several. secondary structure assignment methods are presently available, but DSSP. STRIDE. In fact, most. DSSP assignments. Typically, the 8 DSSP states. However, they do have. Prediction methods, in general, are more. Rost, 1. 99. 4; Cuff, 1. Thus, 3. 10- helices and b- bridges are more difficult to predict. Therefore an alternative. The DSSP method defines a hydrogen bond when the bond energy is below. Coulomb approximation of the hydrogen bond energy (see. SECONDARY STRUCTURE CONCEPTS). The structure assignments are defined such that. In case of overlaps, a- helix is given first priority. This. procedure does not affect the Coulomb approximation, rather the realisation of. An a- helix assignment (DSSP state 'H'). This definition. is also used for 3. G' with i . The helix definition does not. A minimal size helix is set to have two consecutive hydrogen bonds in. T'). b- sheet residues. E') are defined as either having two hydrogen bonds in the sheet, or. This implies three sheet. The minimal sheet consists of two residues at each partner. Isolated residues fulfilling this hydrogen bond criterion are labelled. B'). The recurring. H- bonding patterns connecting the partnering strands in a b- sheet are occasionally interrupted. In DSSP these residues are also assigned as b- sheet 'E' and may comprise up to. The remaining two DSSP states 'S' and ' ' (space) indicate a. Fig. The first two columns contain the unique DSSP residue number and the corresponding PDB residue number. The third column (here empty) indicates the chain identifier if there are multiple chains. Then follows the amino acid 'AA' in one letter codes (note: lower case letters are all Cysteines, in order to match up Cysteine- bridges, e. The 'STRUCTURE' section starts with the secondary structure synopsis (HBEGITS listed in order of priority in case of overlaps) and is followed by helix hydrogen bond indications for 3. X' both. The bend and chirality are each given a column followed by the b- bridge label columns (lower case labels are parallel b- bridges and upper case are anti- parallel).
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