Literature DB >> 1584778

Environment affects amino acid preference for secondary structure.

L Zhong1, W C Johnson.   

Abstract

Three equivocal amino acid sequences were synthesized that are predicted to be alpha-helical from amino acid preference but are found to be primarily beta-strand from x-ray diffraction of their respective proteins. In some solvent systems we recover the alpha-helical structure predicted by amino acid preference, whereas in other systems we mimic the interior of the protein and produce a beta-strand. These results are experimental proof that the environment is important in determining the secondary structure formed by an amino acid sequence; therefore schemes that predict secondary structure from amino acid sequence alone can never be totally successful.

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Year:  1992        PMID: 1584778      PMCID: PMC49102          DOI: 10.1073/pnas.89.10.4462

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  36 in total

Review 1.  Dominant forces in protein folding.

Authors:  K A Dill
Journal:  Biochemistry       Date:  1990-08-07       Impact factor: 3.162

2.  Linear optimization of predictors for secondary structure. Application to transbilayer segments of membrane proteins.

Authors:  J Edelman; S H White
Journal:  J Mol Biol       Date:  1989-11-05       Impact factor: 5.469

Review 3.  Signal sequences.

Authors:  L M Gierasch
Journal:  Biochemistry       Date:  1989-02-07       Impact factor: 3.162

4.  A method to identify protein sequences that fold into a known three-dimensional structure.

Authors:  J U Bowie; R Lüthy; D Eisenberg
Journal:  Science       Date:  1991-07-12       Impact factor: 47.728

5.  Simulations of the folding of a globular protein.

Authors:  J Skolnick; A Kolinski
Journal:  Science       Date:  1990-11-23       Impact factor: 47.728

6.  Predicting the secondary structure of globular proteins using neural network models.

Authors:  N Qian; T J Sejnowski
Journal:  J Mol Biol       Date:  1988-08-20       Impact factor: 5.469

Review 7.  Secondary structure of proteins through circular dichroism spectroscopy.

Authors:  W C Johnson
Journal:  Annu Rev Biophys Biophys Chem       Date:  1988

8.  Stability of phage T4 lysozymes. I. Native properties and thermal stability of wild type and two mutant lysozymes.

Authors:  M L Elwell; J A Schellman
Journal:  Biochim Biophys Acta       Date:  1977-10-26

9.  Structure of the DNA-Eco RI endonuclease recognition complex at 3 A resolution.

Authors:  J A McClarin; C A Frederick; B C Wang; P Greene; H W Boyer; J Grable; J M Rosenberg
Journal:  Science       Date:  1986-12-19       Impact factor: 47.728

10.  Persistence of the alpha-helix stop signal in the S-peptide in trifluoroethanol solutions.

Authors:  J W Nelson; N R Kallenbach
Journal:  Biochemistry       Date:  1989-06-13       Impact factor: 3.162

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  59 in total

1.  Predicting conformational switches in proteins.

Authors:  M Young; K Kirshenbaum; K A Dill; S Highsmith
Journal:  Protein Sci       Date:  1999-09       Impact factor: 6.725

2.  Environmental features are important in determining protein secondary structure.

Authors:  J R Macdonald; W C Johnson
Journal:  Protein Sci       Date:  2001-06       Impact factor: 6.725

3.  Converting the highly amyloidogenic human calcitonin into a powerful fibril inhibitor by three-dimensional structure homology with a non-amyloidogenic analogue.

Authors:  Giuseppina Andreotti; Rosa Maria Vitale; Carmit Avidan-Shpalter; Pietro Amodeo; Ehud Gazit; Andrea Motta
Journal:  J Biol Chem       Date:  2010-11-15       Impact factor: 5.157

4.  Spontaneous fibril formation by polyalanines; discontinuous molecular dynamics simulations.

Authors:  Hung D Nguyen; Carol K Hall
Journal:  J Am Chem Soc       Date:  2006-02-15       Impact factor: 15.419

5.  What determines the structure and stability of KFFE monomers, dimers, and protofibrils?

Authors:  Giovanni Bellesia; Joan-Emma Shea
Journal:  Biophys J       Date:  2009-02       Impact factor: 4.033

6.  Molecular dynamics simulation of surfactin molecules at the water-hexane interface.

Authors:  J P Nicolas
Journal:  Biophys J       Date:  2003-09       Impact factor: 4.033

7.  Biophysical characterization of a recombinant aminopeptidase II from the thermophilic bacterium Bacillus stearothermophilus.

Authors:  Tzu-Fan Wang; Min-Guan Lin; Huei-Fen Lo; Meng-Chun Chi; Long-Liu Lin
Journal:  J Biol Phys       Date:  2013-10-29       Impact factor: 1.365

8.  Membrane-inserted conformation of transmembrane domain 4 of divalent-metal transporter.

Authors:  Hongyan Li; Fei Li; Hongzhe Sun; Zhong Ming Qian
Journal:  Biochem J       Date:  2003-06-15       Impact factor: 3.857

9.  Calcium-dependent association of calmodulin with the rubella virus nonstructural protease domain.

Authors:  Yubin Zhou; Wen-Pin Tzeng; Hing-Cheung Wong; Yiming Ye; Jie Jiang; Yanyi Chen; Yun Huang; Suganthi Suppiah; Teryl K Frey; Jenny J Yang
Journal:  J Biol Chem       Date:  2010-01-19       Impact factor: 5.157

10.  Osmolyte-induced perturbations of hydrogen bonding between hydration layer waters: correlation with protein conformational changes.

Authors:  Feng Guo; Joel M Friedman
Journal:  J Phys Chem B       Date:  2009-12-31       Impact factor: 2.991

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