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Literature DB >> 21523554

Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants.

Mateusz Banach¹, Katarzyna Prymula, Wiktor Jurkowski, Leszek Konieczny, Irena Roterman.

Abstract

Mutations in proteins introduce structural changes and influence biological activity: the specific effects depend on the location of the mutation. The simple method proposed in the present paper is based on a two-step model of in silico protein folding. The structure of the first intermediate is assumed to be determined solely by backbone conformation. The structure of the second one is assumed to be determined by the presence of a hydrophobic center. The comparable structural analysis of the set of mutants is performed to identify the mutant-induced structural changes. The changes of the hydrophobic core organization measured by the divergence entropy allows quantitative comparison estimating the relative structural changes upon mutation. The set of antifreeze proteins, which appeared to represent the hydrophobic core structure accordant with "fuzzy oil drop" model was selected for analysis.

Entities: Chemical Disease Mutation Species

Mesh：

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Year: 2011 PMID： 21523554 PMCID： PMC3249532 DOI： 10.1007/s00894-011-1033-4

Source DB: PubMed Journal: J Mol Model ISSN： 0948-5023 Impact factor: 1.810

16 in total

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Authors: W KAUZMANN
Journal: Adv Protein Chem Date: 1959

2. Gauss-function-Based model of hydrophobicity density in proteins.

Authors: Leszek Konieczny; Michal Brylinski; Irena Roterman
Journal: In Silico Biol Date: 2006

Review 3. The locus of evolution: evo devo and the genetics of adaptation.

Authors: Hopi E Hoekstra; Jerry A Coyne
Journal: Evolution Date: 2007-05 Impact factor: 3.694

4. Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways.

Authors: K Tanuj Sapra; G Prakash Balasubramanian; Dirk Labudde; James U Bowie; Daniel J Muller
Journal: J Mol Biol Date: 2007-12-23 Impact factor: 5.469

5. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids.

Authors: Katarzyna Prymula; Kinga Sałapa; Irena Roterman
Journal: J Mol Model Date: 2010-01-19 Impact factor: 1.810

6. Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding.

Authors: Steven Stayrook; Peera Jaru-Ampornpan; Jenny Ni; Ann Hochschild; Mitchell Lewis
Journal: Nature Date: 2008-04-24 Impact factor: 49.962

7. A simplified representation of protein conformations for rapid simulation of protein folding.

Authors: M Levitt
Journal: J Mol Biol Date: 1976-06-14 Impact factor: 5.469

8. Identification of functional similarities between proteins using directed evolution.

Authors: Daniel Christ; Greg Winter
Journal: Proc Natl Acad Sci U S A Date: 2003-10-22 Impact factor: 11.205

9. An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs.

Authors: Rafael Couñago; Corey J Wilson; Matthew I Peña; Pernilla Wittung-Stafshede; Yousif Shamoo
Journal: Protein Eng Des Sel Date: 2007-12-19 Impact factor: 1.650

Fuzzy oil drop model to interpret the structure of antifreeze proteins and their mutants.

1. Some factors in the interpretation of protein denaturation.

2. Gauss-function-Based model of hydrophobicity density in proteins.

Review 3. The locus of evolution: evo devo and the genetics of adaptation.

4. Point mutations in membrane proteins reshape energy landscape and populate different unfolding pathways.

5. "Fuzzy oil drop" model applied to individual small proteins built of 70 amino acids.

6. Crystal structure of the lambda repressor and a model for pairwise cooperative operator binding.

7. A simplified representation of protein conformations for rapid simulation of protein folding.

8. Identification of functional similarities between proteins using directed evolution.

9. An adaptive mutation in adenylate kinase that increases organismal fitness is linked to stability-activity trade-offs.

10. I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure.

1. Intermediates in the protein folding process: a computational model.

2. Statistical dictionaries for hypothetical in silico model of the early-stage intermediate in protein folding.

3. Structural Interface Forms and Their Involvement in Stabilization of Multidomain Proteins or Protein Complexes.

4. Is the hydrophobic core a universal structural element in proteins?

5. Determining protein similarity by comparing hydrophobic core structure.

6. Towards the design of anti-amyloid short peptide helices.

7. Hypothetical in silico model of the early-stage intermediate in protein folding.