Literature DB >> 7787420

Chemical shifts and three-dimensional protein structures.

E Oldfield1.   

Abstract

During the past three years it has become possible to compute ab initio the 13C, 15N and 19F NMR chemical shifts of many sites in native proteins. Chemical shifts are beginning to become a useful supplement to more established methods of solution structure determination, and may find utility in solid-state analysis as well. From 13C NMR, information on phi, psi and chi torsions can be obtained, permitting both assignment verification, and structure refinement and prediction. For 15N, both torsional and hydrogen-bonding effects are important, while for 19F, chemical shifts are primarily indicators of the local charge field. Chemical shift calculations are still slow, but shielding hypersurfaces - the shift as a function of the dihedral angles that define the molecular conformation - are becoming accessible. Over the next few years, theoretical and computer hardware improvements will enable more routine use of chemical shifts in structural studies, including the study of metal-ligand interactions, the analysis of drug and substrate binding and catalysis, the study of folding/unfolding pathways, as well as the characterization of conformational substates. Rather than simply being a necessary prerequisite for multidimensional NMR, chemical shifts and chemical shift non-equivalence due to folding are now beginning to be useful for structural characterization.

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Year:  1995        PMID: 7787420     DOI: 10.1007/bf00211749

Source DB:  PubMed          Journal:  J Biomol NMR        ISSN: 0925-2738            Impact factor:   2.835


  15 in total

1.  Demonstration by NMR of folding domains in lysozyme.

Authors:  A Miranker; S E Radford; M Karplus; C M Dobson
Journal:  Nature       Date:  1991-02-14       Impact factor: 49.962

2.  The chemical shift index: a fast and simple method for the assignment of protein secondary structure through NMR spectroscopy.

Authors:  D S Wishart; B D Sykes; F M Richards
Journal:  Biochemistry       Date:  1992-02-18       Impact factor: 3.162

3.  NMR structure-based drug design.

Authors:  S W Fesik
Journal:  J Biomol NMR       Date:  1993-05       Impact factor: 2.835

4.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

Authors:  J W Ponder; F M Richards
Journal:  J Mol Biol       Date:  1987-02-20       Impact factor: 5.469

Review 5.  Prospects for NMR of large proteins.

Authors:  G Wagner
Journal:  J Biomol NMR       Date:  1993-07       Impact factor: 2.835

6.  The impact of direct refinement against 13C alpha and 13C beta chemical shifts on protein structure determination by NMR.

Authors:  J Kuszewski; J Qin; A M Gronenborn; G M Clore
Journal:  J Magn Reson B       Date:  1995-01

7.  Comparison of four independently determined structures of human recombinant interleukin-4.

Authors:  L J Smith; C Redfield; R A Smith; C M Dobson; G M Clore; A M Gronenborn; M R Walter; T L Naganbushan; A Wlodawer
Journal:  Nat Struct Biol       Date:  1994-05

8.  Combined use of 13C chemical shift and 1H alpha-13C alpha heteronuclear NOE data in monitoring a protein NMR structure refinement.

Authors:  B Celda; C Biamonti; M J Arnau; R Tejero; G T Montelione
Journal:  J Biomol NMR       Date:  1995-02       Impact factor: 2.835

9.  The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data.

Authors:  D S Wishart; B D Sykes
Journal:  J Biomol NMR       Date:  1994-03       Impact factor: 2.835

10.  Secondary and tertiary structural effects on protein NMR chemical shifts: an ab initio approach.

Authors:  A C de Dios; J G Pearson; E Oldfield
Journal:  Science       Date:  1993-06-04       Impact factor: 47.728

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  46 in total

1.  Conformational ensembles: the role of neuropeptide structures in receptor binding.

Authors:  A S Edison; E Espinoza; C Zachariah
Journal:  J Neurosci       Date:  1999-08-01       Impact factor: 6.167

2.  Application of automated NOE assignment to three-dimensional structure refinement of a 28 kDa single-chain T cell receptor.

Authors:  B J Hare; G Wagner
Journal:  J Biomol NMR       Date:  1999-10       Impact factor: 2.835

3.  Alignment of weakly interacting molecules to protein surfaces using simulations of chemical shift perturbations.

Authors:  M A McCoy; D F Wyss
Journal:  J Biomol NMR       Date:  2000-11       Impact factor: 2.835

4.  13C(alpha) and 13C(beta) chemical shifts as a tool to delineate beta-hairpin structures in peptides.

Authors:  C M Santiveri; M Rico; M A Jiménez
Journal:  J Biomol NMR       Date:  2001-04       Impact factor: 2.835

5.  PROSHIFT: protein chemical shift prediction using artificial neural networks.

Authors:  Jens Meiler
Journal:  J Biomol NMR       Date:  2003-05       Impact factor: 2.835

6.  C(alpha) chemical shift tensors in helical peptides by dipolar-modulated chemical shift recoupling NMR.

Authors:  Xiaolan Yao; Satoru Yamaguchi; Mei Hong
Journal:  J Biomol NMR       Date:  2002-09       Impact factor: 2.835

7.  An empirical correlation between secondary structure content and averaged chemical shifts in proteins.

Authors:  Anaika B Sibley; Monique Cosman; V V Krishnan
Journal:  Biophys J       Date:  2003-02       Impact factor: 4.033

8.  Assignment validation software suite for the evaluation and presentation of protein resonance assignment data.

Authors:  Hunter N B Moseley; Gurmukh Sahota; Gaetano T Montelione
Journal:  J Biomol NMR       Date:  2004-04       Impact factor: 2.835

9.  Conformational distributions of denatured and unstructured proteins are similar to those of 20 × 20 blocked dipeptides.

Authors:  Kwang-Im Oh; Young-Sang Jung; Geum-Sook Hwang; Minhaeng Cho
Journal:  J Biomol NMR       Date:  2012-03-18       Impact factor: 2.835

10.  Analysis of (1)H chemical shifts in DNA: Assessment of the reliability of (1)H chemical shift calculations for use in structure refinement.

Authors:  S S Wijmenga; M Kruithof; C W Hilbers
Journal:  J Biomol NMR       Date:  1997-12       Impact factor: 2.835

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