TITLE

Correlations between designability and various structural characteristics of protein lattice models

AUTHOR(S)
Jian-Yi Yang; Zu-Guo Yu; Vo Anh
PUB. DATE
May 2007
SOURCE
Journal of Chemical Physics;5/21/2007, Vol. 126 Issue 19, p195101
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Using six kinds of lattice types (4×4, 5×5, and 6×6 square lattices; 3×3×3 cubic lattice; and 2+3+4+3+2 and 4+5+6+5+4 triangular lattices), three different size alphabets (HP, HNUP, and 20 letters), and two energy functions, the designability of protein structures is calculated based on random samplings of structures and common biased sampling (CBS) of protein sequence space. Then three quantities stability (average energy gap), foldability, and partnum of the structure, which are defined to elucidate the designability, are calculated. The authors find that whatever the type of lattice, alphabet size, and energy function used, there will be an emergence of highly designable (preferred) structure. For all cases considered, the local interactions reduce degeneracy and make the designability higher. The designability is sensitive to the lattice type, alphabet size, energy function, and sampling method of the sequence space. Compared with the random sampling method, both the CBS and the Metropolis Monte Carlo sampling methods make the designability higher. The correlation coefficients between the designability, stability, and foldability are mostly larger than 0.5, which demonstrate that they have strong correlation relationship. But the correlation relationship between the designability and the partnum is not so strong because the partnum is independent of the energy. The results are useful in practical use of the designability principle, such as to predict the protein tertiary structure.
ACCESSION #
25183159

 

Related Articles

  • Nonlinear Marangoni convection in circular and elliptical cylinders. Assemat, P.; Bergeon, A.; Knobloch, E. // Physics of Fluids;Oct2007, Vol. 19 Issue 10, p104101 

    The spatial organization of single-fluid Marangoni convection in vertical cylinders with circular or elliptical horizontal cross section is described. The convection is driven by an imposed heat flux from above through Marangoni stresses at a free but undeformed surface due to...

  • Nuclear recoil effect on the magnetic-dipole decay rates of atomic levels. Volotka, A. V.; Glazov, D. A.; Plunien, G.; Shabaev, V. M.; Tupitsyn, I. I. // European Physical Journal D -- Atoms, Molecules, Clusters & Opti;Nov2008, Vol. 48 Issue 2, p167 

    The effect of finite nuclear mass on the magnetic-dipole transition probabilities between fine-structure levels of the same term is investigated. Based on a rigorous QED approach a nonrelativistic formula for the recoil correction to first order in me/M is derived. Numerical results for...

  • Relations between coordinate and potential scaling in the high-density limit. Whittingham, Takeyce K.; Burke, Kieron // Journal of Chemical Physics;4/1/2005, Vol. 122 Issue 13, p134108 

    Exact relations are derived between scaling to the high-density limit of density functional theory and taking Z to infinity for nondegenerate atoms. Görling–Levy perturbation results are deduced for hydrogenic densities. The kinetic contribution to the correlation energy is also...

  • Gauge supersymmetric Ising model on a cubic lattice near the critical point in the free field representation. Vergeles, S. // JETP Letters;Sep2012, Vol. 96 Issue 2, p123 

    The nature of the set of free fields that represent the system at the critical point has been revealed by studying the correlation functions of the degrees of freedom of the gauge supersymmetric Ising model on the cubic lattice. The same set of free fields represents the continuous...

  • Computational classification of microRNAs in next-generation sequencing data. Riback, Joshua; Hatzigeorgiou, Artemis G.; Reczko, Martin // Theoretical Chemistry Accounts: Theory, Computation, & Modeling;Mar2010, Vol. 125 Issue 3-6, p637 

    MicroRNAs (miRNAs) have been shown to play an important regulatory role in plants and animals. A large number of known and novel miRNAs can be uncovered from next-generation sequencing (NGS) experiments that measure the complement of a given cell’s small RNAs under various conditions....

  • Why similar protein sequences encode similar three-dimensional structures? Kaczanowski, Szymon; Zielenkiewicz, Piotr // Theoretical Chemistry Accounts: Theory, Computation, & Modeling;Mar2010, Vol. 125 Issue 3-6, p643 

    Evolutionarily related proteins have similar sequences. Such similarity is called homology and can be described using substitution matrices such as Blosum 60. Naturally occurring homologous proteins usually have similar stable tertiary structures and this fact is used in so-called homology...

  • SCPRED: Accurate prediction of protein structural class for sequences of twilight-zone similarity with predicting sequences. Kurgan, Lukasz; Cios, Krzysztof; Ke Chen // BMC Bioinformatics;2008, Vol. 9, Special section p1 

    Background: Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains that share twilight-zone pairwise identity can form similar folds and thus...

  • Generic coarse-grained model for protein folding and aggregation. Bereau, Tristan; Deserno, Markus // Journal of Chemical Physics;6/21/2009, Vol. 130 Issue 23, p235106 

    A generic coarse-grained (CG) protein model is presented. The intermediate level of resolution (four beads per amino acid, implicit solvent) allows for accurate sampling of local conformations. It relies on simple interactions that emphasize structure, such as hydrogen bonds and hydrophobicity....

  • Functional Identification of Close Proximity Amino Acid Side Chains within the Transmembrane-Spanning Helixes of the P2X2 Receptor. Liang, Xin; Xu, Huijuan; Li, Caiyue; Yin, Shikui; Xu, Tingting; Liu, Jinsong; Li, Zhiyuan // PLoS ONE;Aug2013, Vol. 8 Issue 8, p1 

    The transition from the closed to open state greatly alters the intra- and inter-subunit interactions of the P2X receptor (P2XR). The interactions that occur in the transmembrane domain of the P2X2R remain unclear. We used substituted cysteine mutagenesis disulfide mapping to identify pairs of...

Share

Read the Article

Courtesy of VIRGINIA BEACH PUBLIC LIBRARY AND SYSTEM

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics