Proteins: coexistence of stability and flexibility

@article{Reuveni2008ProteinsCO,
  title={Proteins: coexistence of stability and flexibility},
  author={Shlomi Reuveni and Rony Granek and Joseph Klafter},
  journal={Physical review letters},
  year={2008},
  volume={100 20},
  pages={
          208101
        }
}
We introduce an equation for protein native topology based on recent analysis of data from the Protein Data Bank and on a generalization of the Landau-Peierls instability criterion for fractals. The equation relates the protein fractal dimension df, the spectral dimension ds, and the number of amino acids N. Deviations from the equation may render a protein unfolded. The fractal nature of proteins is shown to bridge their seemingly conflicting properties of stability and flexibility. Over 500… Expand
Coexistence of Flexibility and Stability of Proteins: An Equation of State
TLDR
A recently suggested “equation of state” for natively folded proteins is considered, and its validity is verified for a set of about 5800 proteins, and it is demonstrated that the equation of state is well obeyed. Expand
Fractal protein structure revisited: Topological, kinetic and thermodynamic relationships
The present work explored the definitions and calculations of fractal dimensions in protein structures and the corresponding relationships with the protein class, secondary structure contents, foldExpand
Fractals and self-organized criticality in proteins
Self-organized criticality, a powerful concept, originated in 1987 as an extension of fractal geometries to thermodynamic systems in the vicinities of instabilities. The value of fractal methods canExpand
Dynamic structure factor of vibrating fractals: proteins as a case study.
TLDR
Experiments in which the rotational and translational degrees of freedom are arrested, e.g., by anchoring the proteins to a surface, will improve the detection of internal vibrational dynamics, and an effective stretched exponential decay of the dynamic structure factor is found. Expand
Long-Range Structural Regularities and Collectivity of Folded Proteins
Coarse-grained network models of proteins successfully predict equilibrium properties related to collective modes of motion. In this study, the network construction strategies and their systematicExpand
Protein sequence complexity revisited. Relationship with fractal 3D structure, topological and kinetic parameters
Abstract The study of protein sequence complexity is not a new area and several methodological approaches are available in order to describe or represent the protein sequence information. The presentExpand
Long-range correlation in protein dynamics: Confirmation by structural data and normal mode analysis
TLDR
This work demonstrates that long-range correlations of proteins contribute to many biological processes such as allostery, catalysis, and transportation are encoded in the native topology of the proteins, and quantitatively describes how native proteins balance between order and disorder. Expand
Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure
TLDR
This work uses diffusion, a method sensitive to the structural features of the protein fold and them alone, in order to probe protein structure and finds it to be anomalous, an indication of a fractal-like structure. Expand
Critical Fluctuations in the Native State of Proteins.
TLDR
The results suggest that the protein's native state is critical, and that proteins with larger susceptibility are more frequently observed in nature. Expand
Revisiting the Myths of Protein Interior: Studying Proteins with Mass-Fractal Hydrophobicity-Fractal and Polarizability-Fractal Dimensions
TLDR
It is found that (barring ‘all-α’) all the major structural classes of proteins have an amount of unused hydrophobicity left in them, and it is shown that myths regarding protein interior organization might obfuscate knowledge of actual reality. Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 48 REFERENCES
Introduction to percolation theory
Preface to the Second Edition Preface to the First Edition Introduction: Forest Fires, Fractal Oil Fields, and Diffusion What is percolation? Forest fires Oil fields and fractals Diffusion inExpand
Macromolecules
  • C. Tanford
  • Medicine
  • Protein science : a publication of the Protein Society
  • 1948
TLDR
The formation of a glycosidic linkage is described and the four levels of protein structure are described. Expand
Biochemistry
The Department of Biochemistry is internationally recognized for its research and education and offers a world-class interdisciplinary research environment in a beautiful mountain setting. As part ofExpand
Nature
  • R. Rosenfeld
  • Medicine
  • Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery
  • 2009
TLDR
I am writing with a simple plea to balance the voluminous articles about treatment in your journal with a modicum of information about nature and caring effects to rekindle the perception of physicians as healers, not only treaters, who relish the gifts of nature, and foster the humanistic aspect of medicine that has thrived for millennia. Expand
疟原虫var基因转换速率变化导致抗原变异[英]/Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A
抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1(PfPMP1)与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用,在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员,通过启动转录不同的var基因变异体为抗原变异提供了分子基础。
Folding Des
  • 2, 173
  • 1997
PRL
  • PRL
  • 2008
Proc
  • Natl. Acad. Sci. U.S.A. 104, 8803 (2007). PRL 100, 208101
  • 2008
Structure
  • Structure
  • 2007
Structure 15
  • 741
  • 2007
...
1
2
3
4
5
...