Side-chain conformation angles of amino acids: effect of temperature factor cut-off

Bhargavi, G. Ramya; Sheik, S. S.; Velmurugan, D.; Sekar, K.

doi:10.1016/j.jsb.2003.08.003

Cited by 7 publications

(8 citation statements)

References 13 publications

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“…In the present study, POG3‐PRG‐POG4 contains four independent arginine residues, ArgA11, ArgB11a, ArgB11b, and ArgC11 (Table ), of which ArgB11 has a different side‐chain conformation. Because each of these four angles can be classified into three rotameric conformations, gauche + ( g + ), gauche − ( g − ), and trans ( t ), the side‐chain conformations of the ArgA11, ArgB11a, ArgB11b, and ArgC11 residues can be designated as ttg − t , tg − g − t , ttg − t , and ttg − t , respectively. As an example of a ttg − t conformation, the side chain of ArgA11 is shown in Figure ; in this, the side‐chain atoms are in close contact with the C γ atom of ProB10, the carbonyl oxygen of ArgB11, the C α and C' atoms of GlyB12, and the C δ and C γ atoms of ProB13 in the adjacent strand.…”

Section: Resultsmentioning

confidence: 99%

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

et al. 2014

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The crystal structure of the triple-helical peptide (Pro-Hyp-Gly)3 -Pro-Arg-Gly-(Pro-Hyp-Gly)4 (POG3-PRG-POG4) was determined at 1.45 Å resolution. POG3-PRG-POG4 was designed to permit investigation of the side-chain conformation of the Arg residues in a triple-helical structure. Because of the alternative structure of one of three Arg residues, four side-chain conformations were observed in an asymmetric unit. Among them, three adopt a ttg(-) t conformation and the other adopts a tg(-) g(-) t conformation. A statistical analysis of 80 Arg residues in various triple-helical peptides showed that, unlike those in globular proteins, they preferentially adopt a tt conformation for χ1 and χ2 , as observed in POG3-PRG-POG4. This conformation permits van der Waals contacts between the side-chain atoms of Arg and the main-chain atoms of the adjacent strand in the same molecule. Unlike many other host-guest peptides, in which there is a significant difference between the helical twists in the guest and the host peptides, POG3-PRG-POG4 shows a marked difference between the helical twists in the N-terminal peptide and those in the C-terminal peptide, separated near the Arg residue. This suggested that the unique side-chain conformation of the Arg residue affects not only the conformation of the guest peptide, but also the conformation of the peptide away from the Arg residue.

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Section: Resultsmentioning

confidence: 99%

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

et al. 2014

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“…The superposition of an ensemble of NMR models can indicate the existence of unambiguous conformations of surface side chains 21, 22. Such conformations generally have relatively low temperature factors in X‐ray structures 23. Furthermore, since we define surface side chains here as those more than 50% exposed, most surface side chains experience some motional hindrance, and their conformations are predictable to some extent.…”

Section: Introductionmentioning

confidence: 99%

Prediction of side‐chain conformations on protein surfaces

et al. 2007

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An approach is described that improves the prediction of the conformations of surface side chains in crystal structures, given the main-chain conformation of a protein. A key element of the methodology involves the use of the colony energy. This phenomenological term favors conformations found in frequently sampled regions, thereby approximating entropic effects and serving to smooth the potential energy surface. Use of the colony energy significantly improves prediction accuracy for surface side chains with little additional computational cost. Prediction accuracy was quantified as the percentage of side-chain dihedral angles predicted to be within 40°o f the angles measured by X-ray diffraction. Use of the colony energy in predictions for single side chains improved the prediction accuracy for χ 1 and χ 1+2 from 65 and 40% to 74 and 59%, respectively. Several other factors that affect prediction of surface side-chain conformations were also analyzed, including the extent of conformational sampling, details of the rotamer library employed, and accounting for the crystallographic environment. The prediction of conformations for polar residues on the surface was generally found to be more difficult than those for hydrophobic residues, except for polar residues participating in hydrogen bonds with other protein groups. For surface residues with hydrogen-bonded side chains, the prediction accuracy of χ 1 and χ 1+2 was 79 and 63%, respectively. For surface polar residues, in general (all side-chain prediction), the accuracy of χ 1 and χ 1+2 was only 73 and 56%, respectively. The most accurate results were obtained using the colony energy and an all-atom description that includes neighboring molecules in the crystal (protein chains and hetero atoms). Here, the accuracy of χ 1 and χ 1+2 predictions for surface side chains was 82 and 73%, respectively. The root mean square deviations obtained for hydrogen-bonding surface side chains were 1.64 and 1.81 Å, with and without consideration of crystal packing effects, respectively.

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“…According to a statistical analysis, the g + conformation of χ 1 for Asp residues should be the most frequently observed conformation among the three expected conformations: g + , g − , and t . When χ 1 adopts the g + conformation, the cis conformation of χ 2 is also frequently observed . Therefore, the side‐chain conformation of the three Asp residues in the PPG9‐ODG peptide follows the general trend that has been observed in many other proteins.…”

Section: Resultsmentioning

confidence: 71%

“…The side‐chain conformation angles of aspartic acid residues χ 1 (N–C α –C β –C γ ) and χ 2 (C α –C β –C γ –O δ1 ) were −72.69° and 10.82°, respectively, for AspA14; −58.17° and −28.53°, respectively, for AspB14; and −68.09° and 12.55°, respectively, for AspC14. According to a statistical analysis, the g + conformation of χ 1 for Asp residues should be the most frequently observed conformation among the three expected conformations: g + , g − , and t . When χ 1 adopts the g + conformation, the cis conformation of χ 2 is also frequently observed .…”

Section: Resultsmentioning

confidence: 99%

Crystal structure of the collagen model peptide (Pro‐Pro‐Gly)₄‐Hyp‐Asp‐Gly‐(Pro‐Pro‐Gly)₄ at 1.0 Å resolution

et al. 2013

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The single-crystal structure of the collagen-like peptide (Pro-Pro-Gly)4 -Hyp-Asp-Gly-(Pro-Pro-Gly)4, was analyzed at 1.02 Å resolution. The overall average helical twist (θ = 49.6°) suggests that this peptide adopts a 7/2 triple-helical structure and that its conformation is very similar to that of (Gly-Pro-Hyp)9, which has the typical repeating sequence in collagen. High-resolution studies on other collagen-like peptides have shown that imino acid-rich sequences preferentially adopt a 7/2 triple-helical structure (θ = 51.4°), whereas imino acid-lean sequences adopt relaxed conformations (θ < 51.4°). The guest Gly-Hyp-Asp sequence in the present peptide, however, has a large helical twist (θ = 61.1°), whereas that of the host Pro-Pro-Gly sequence is small (θ = 46.7°), indicating that the relationship between the helical conformation and the amino acid sequence of such peptides is complex. In the present structure, a strong intermolecular hydrogen bond between two Asp residues on the A and B strands might induce the large helical twist of the guest sequence; this is compensated by a reduced helical twist in the host, so that an overall 7/2-helical symmetry is maintained. The Asp residue in the C strand might interact electrostatically with the N-terminus of an adjacent molecule, causing axial displacement, reminiscent of the D-staggered structure in fibrous collagens.

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Side-chain conformation angles of amino acids: effect of temperature factor cut-off

Cited by 7 publications

References 13 publications

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

Prediction of side‐chain conformations on protein surfaces

Crystal structure of the collagen model peptide (Pro‐Pro‐Gly)₄‐Hyp‐Asp‐Gly‐(Pro‐Pro‐Gly)₄ at 1.0 Å resolution

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Side-chain conformation angles of amino acids: effect of temperature factor cut-off

Cited by 7 publications

References 13 publications

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

Preferred side‐chain conformation of arginine residues in a triple‐helical structure

Prediction of side‐chain conformations on protein surfaces

Crystal structure of the collagen model peptide (Pro‐Pro‐Gly)4‐Hyp‐Asp‐Gly‐(Pro‐Pro‐Gly)4 at 1.0 Å resolution

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Crystal structure of the collagen model peptide (Pro‐Pro‐Gly)₄‐Hyp‐Asp‐Gly‐(Pro‐Pro‐Gly)₄ at 1.0 Å resolution