Improving the efficiency of protein structure determination from NMR

Kirnarsky, Leonid; Shats, Oleg; Sherman, Simon

doi:10.1016/s0166-1280(97)00196-6

Cited by 5 publications

(5 citation statements)

References 26 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…For each structural family, the ‘overall precision’ (19) and average structures were calculated as described previously (10). Using the CLUSTER procedure (10), the backbone atoms of the PLaR residues of each structure were overlaid to evaluate similarities in this region of YSFKPMPLaR.…”

Section: Methodsmentioning

confidence: 99%

“…To generate the three‐dimensional structure of YSFKPMPLaR, the previously described structure determination protocol was used (10). The COMBINE procedure (18), utilizing the FiSiNOE‐3 (19) and HABAS (20) computer programs, was used to determine the ranges for the φ, ψ, and χ 1 angles for each residue in the peptide, and to make stereospecific assignments of the β‐methylene protons. The information determined by the COMBINE procedure, in conjunction with the NOE distance constraints, was used as input data for the DIANA program (utilizing the REDAC strategy; 20) to generate 100 structures consistent with the NMR data set.…”

Section: Methodsmentioning

confidence: 99%

“…To generate the three-dimensional structure of YSFKPM-PLaR, the previously described structure determination protocol was used (10). The COMBINE procedure (18), utilizing the FiSiNOE-3 (19) and HABAS (20) computer programs, was used to determine the ranges for the w, y, and…”

Section: Structure Determination Protocolmentioning

confidence: 99%

See 2 more Smart Citations

Determination of structural elements related to the biological activities of a potent decapeptide agonist of human C5a anaphylatoxin

Vogen

Prakash

Kirnarsky

et al. 1999

The Journal of Peptide Research

View full text Add to dashboard Cite

The structural features related to the biologic activities of a potent, response-selective decapeptide agonist of human C5a, YSFKPMPLaR (C5a65-74, Y65, F67, P69, P71, D-Ala73), were identified by NMR analysis in H2O, DMSO and TFE. This investigation showed that the KPM residues in H2O and the SFKPM residues in DMSO exhibited an extended backbone conformation, whereas a twisted conformation was found in this region in TFE. In H2O, the C-terminal region (PLaR) adopted a distorted type II beta-turn or a type II/V beta-turn. In the type IIN beta-turn, Leu72 exhibited a conformation typical of a type II beta-turn, whereas D-Ala73 exhibited a conformation characteristic of a type V beta-turn. Furthermore, a gamma-turn involving residues LaR overlapped with the type II/V beta-turn. In DMSO, the C-terminal region had the analogous turn-like motif (type II/V beta-turn overlapping with gamma-turn) found in H2O. In TFE, no beta-turn motifs were formed by the PLaR residues. These turn-like motifs in the C-terminal region of the peptide in both H2O and DMSO were in agreement with the biologically important conformations predicted earlier by a structure-function analysis of a related panel of decapeptide analogs. The motifs determined by the NMR analysis of YSFKPMPLaR in H2O and DMSO may represent structural elements important for C5a agonist activity and thus can be used to design the next generation of C5a agonist, partial agonist and antagonist analogs.

show abstract

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Determination of structural elements related to the biological activities of a potent decapeptide agonist of human C5a anaphylatoxin

Vogen

Prakash

Kirnarsky

et al. 1999

The Journal of Peptide Research

View full text Add to dashboard Cite

show abstract

“…The COMBINE procedure (13) was used to determine the ranges for the $, w and x, angles for each residue in the peptide and to make stereospecific assignments of the P-methylene protons. In the first step of the COMBINE procedure, the computer program FiSiNOE-3 (14)…”

Section: Structure Determination Protocolmentioning

confidence: 99%

“…The "overall precision" within each structural family was determined as the root-mean-square deviation (RMSD) of the backbone (C", C' and N) atomic coordinates in the structures and the analogous atoms in the corresponding average structure (14). The average structure was calculated by superimposing and averaging the corresponding atomic coordinates within the family of structures.…”

Section: Structure Analysismentioning

confidence: 99%

NMR analysis of a potent decapeptide agonist of human C5a anaphylatoxin

Vogen

Prakash

Kirnarsky

et al. 1998

The Journal of Peptide Research

Self Cite

View full text Add to dashboard Cite

A NMR investigation in H20, TFE and DMSO of a conformationally constrained, potent decapeptide agonist of human C5a, YSFKDMPLaR (C5a65‐74, Y65, F67, P71, d‐Ala73) showed that its N‐terminal region (YSFKD) exhibited an extended backbone conformation in H2O and a more twisted conformation in both TFE/H2O (30:70, v/v; referred to as TFE) and DMSO. The C‐terminal region (MPLaR) of the peptide adopted compact, turn‐like structures. In H2O, the C‐terminal region adopted a type II β‐turn or a distorted type V/II β‐turn involving residues PLaR. In the distorted type V/II β‐turn, Leu72 exhibited a conformation typical of a type V β‐turn, whereas D‐Ala73 exhibited a conformation typical of a type II β‐turn. The distorted type V/II β‐turn overlapped with an inverse γ‐turn involving residues MPL. In DMSO, the C‐terminal region had the analogous inverse y‐turn and the V/II γ‐turn found in H2O. In many of the DMSO structures, two inverse γ‐turns in the MPL and PLa positions formed a double‐inverse γ‐turn. None of the turns observed in H2O were present in TFE. However, in TFE, the PLa residues formed an inverse γ‐turn. Overall, the turn‐like structural motifs in the C‐terminal region of the peptide in both H2O and DMSO (but not in TFE) agreed with the biologically important conformations obtained earlier by the structure‐function analysis of a panel of C5a agonist peptides. These motifs may represent key structural elements important for C5a agonist activity and may be used to design the next generation of C5a agonist and antagonist analogues. © Munksgaard 1998.

show abstract

A priori and a posteriori mixture distributions for using databases in protein structure determination

Sclove¹,

Sherman²

1997

Journal of Molecular Structure: THEOCHEM

View full text Add to dashboard Cite

Improving the efficiency of protein structure determination from NMR

Cited by 5 publications

References 26 publications

Determination of structural elements related to the biological activities of a potent decapeptide agonist of human C5a anaphylatoxin

Determination of structural elements related to the biological activities of a potent decapeptide agonist of human C5a anaphylatoxin

NMR analysis of a potent decapeptide agonist of human C5a anaphylatoxin

A priori and a posteriori mixture distributions for using databases in protein structure determination

Contact Info

Product

Resources

About