Structure Motivator: A tool for exploring small three-dimensional elements in proteins

Leader, David P.; Milner‐White, E. James

doi:10.1186/1472-6807-12-26

Cited by 9 publications

(11 citation statements)

References 27 publications

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“…Residues within β-turns also adopt spe- f Modification of the dihedral angle sampling of a given residue can be achieved by combining the random coil distribution with an over-sampling of other regions of Ramachandran space (in this case the α-helical region). Dihedral angles for (a), (b) and (e) were extracted from the database embedded in the structure motivator application (Leader and Milner-White 2012). Dihedral angles in (c) were extracted from parallel and anti-parallel β-strands from structures with the following PDB codes: 1MLD, 1QCZ, 2CMD, 1XH3, 1OGT and 3GP6.…”

Section: Local Structure In Idps Can Be Described By the Dihedral Angmentioning

confidence: 99%

Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters

Kragelj

Blackledge

Jensen

2015

Advances in Experimental Medicine and Biology

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Intrinsically disordered proteins (IDPs) perform their function despite their lack of well-defined tertiary structure. Residual structure has been observed in IDPs, commonly described as transient/dynamic or expressed in terms of fractional populations. In order to understand how the protein primary sequence dictates the dynamic and structural properties of IDPs and in general to understand how IDPs function, atomic-level descriptions are needed. Nuclear magnetic resonance spectroscopy provides information about local and long-range structure in IDPs at amino acid specific resolution and can be used in combination with ensemble descriptions to represent the dynamic nature of IDPs. In this chapter we describe sample-and-select approaches for ensemble modelling of local structural propensities in IDPs with specific emphasis on validation of these ensembles.

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Section: Local Structure In Idps Can Be Described By the Dihedral Angmentioning

confidence: 99%

Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters

Kragelj

Blackledge

Jensen

2015

Advances in Experimental Medicine and Biology

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“…This database, in which the structures are corrected for amide atom misplacement in asparagines and glutamines, includes the dihedral angles of the residues and the hydrogen bonds in the protein (derived using the program HBPlus) allowing SQL queries to be made for structures defined by these parameters. The results of queries were analyzed in spreadsheets, and data loaded into the program, Structure Motivator, which allows selection of sub‐structures with specific combinations of dihedral angles.…”

Section: Methodsmentioning

confidence: 99%

Bridging of partially negative atoms by hydrogen bonds from main‐chain NH groups in proteins: The crown motif

Leader

Milner‐White

2015

Proteins

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The backbone NH groups of proteins can form N1N3-bridges to δ-ve or anionic acceptor atoms when the tripeptide in which they occur orients them appropriately, as in the RL and LR nest motifs, which have dihedral angles 1,2-αR αL and 1,2-αL αR , respectively. We searched a protein database for structures with backbone N1N3-bridging to anionic atoms of the polypeptide chain and found that RL and LR nests together accounted for 92% of examples found (88% RL nests, 4% LR nests). Almost all the remaining 8% of N1N3-bridges were found within a third tripeptide motif which has not been described previously. We term this a "crown," because of the disposition of the tripeptide CO groups relative to the three NH groups and the acceptor oxygen anion, and the crown together with its bridged anion we term a "crown bridge." At position 2 of these structures the dihedral angles have a tight αR distribution, but at position 1 they have a wider distribution, with ϕ and ψ values generally being lower than those at position 1. Over half of crown bridges involve the backbone CO group three residues N-terminal to the tripeptide, the remainder being to other main-chain or side-chain carbonyl groups. As with nests, bridging of crowns to oxygen atoms within ligands was observed, as was bridging to the sulfur atom of an iron-sulfur cluster. This latter property may be of significance for protein evolution.

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“…The program developed to analyze the hydrogen bond arrangement in nests was written in Java and used the following strategy. The nests analyzed were 3‐residue motifs of the type 1,2‐α R α L (RL) or 1,2‐α L α R (LR) included in a modified version of the Protein Motif database, which is derived from 429 high resolution nonredundant soluble protein crystal structures . The range of values used to define α R was −140° < ϕ < –20°, −90° < ψ < 40° and that used to define α L was 20° < ϕ < 140°, −40° < ψ < 90°.…”

Section: Methodsmentioning

confidence: 99%

“…Previously our picture of bridging in nests was confined to generalizations resulting from instances examined by molecular graphics. We have, therefore, written a computer program using both distance and orientation criteria in defining hydrogen bonds, and used it to analyze the hydrogen bond arrangement in the nests derived from the 429 proteins in our relational database . We have focused especially on bridges where two NH groups are hydrogen bonded to the same acceptor oxygen atom, allowing us to identify the anion‐binding nests in these proteins, and to determine their abundance and characteristics.…”

Section: Introductionmentioning

confidence: 99%

“…We have, therefore, written a computer program using both distance and orientation criteria 35 in defining hydrogen bonds, and used it to analyze the hydrogen bond arrangement in the nests derived from the 429 proteins in our relational database. 36 We have focused especially on bridges where two NH groups are hydrogen bonded to the same acceptor oxygen atom, allowing us to identify the anion-binding nests in these proteins, and to determine their abundance and characteristics. As the relational database contains the other hydrogen-bonded motifs mentioned above, we have also been able to examine the occurrence of nests containing bridged anions within these motifs.…”

Section: Introductionmentioning

confidence: 99%

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Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins

et al. 2014

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The nest is a protein motif of three consecutive amino acid residues with dihedral angles 1,2-αR αL (RL nests) or 1,2-αL αR (LR nests). Many nests form a depression in which an anion or δ-negative acceptor atom is bound by hydrogen bonds from the main chain NH groups. We have determined the extent and nature of this bridging in a database of protein structures using a computer program written for the purpose. Acceptor anions are bound by a pair of bridging hydrogen bonds in 40% of RL nests and 20% of LR nests. Two thirds of the bridges are between the NH groups at Positions 1 and 3 of the motif (N1N3-bridging)-which confers a concavity to the nest; one third are of the N2N3 type-which does not. In bridged LR nests N2N3-bridging predominates (14% N1N3: 75% N2N3), whereas in bridged RL nests the reverse is true (69% N1N3: 25% N2N3). Most bridged nests occur within larger motifs: 45% in (hexapeptide) Schellman loops with an additional 4 → 0 hydrogen bond (N1N3), 11% in Schellman loops with an additional 5 → 1 hydrogen bond (N2N3), 12% in a composite structure including a type 1β-bulge loop and an asx- or ST- motif (N1N3)-remarkably homologous to the N1N3-bridged Schellman loop-and 3% in a composite structure including a type 2β-bulge loop and an asx-motif (N2N3). A third hydrogen bond is a previously unrecognized feature of Schellman loops as those lacking bridged nests have an additional 4 → 0 hydrogen bond.

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Structure Motivator: A tool for exploring small three-dimensional elements in proteins

Cited by 9 publications

References 27 publications

Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters

Ensemble Calculation for Intrinsically Disordered Proteins Using NMR Parameters

Bridging of partially negative atoms by hydrogen bonds from main‐chain NH groups in proteins: The crown motif

Bridging of anions by hydrogen bonds in nest motifs and its significance for Schellman loops and other larger motifs within proteins

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