相关论文: Geometry Selects Highly Designable Structures

We examined what determines the designability of 2-letter codes (H and P) lattice proteins from three points of view. First, whether the native structure is searched within all possible structures or within maximally compact structures.…

By exact computer enumeration and combinatorial methods, we have calculated the designability of proteins in a simple lattice H-P model for the protein folding problem. We show that if the strength of the non-additive part of the…

We study the designability of all compact 3x3x3 and 6x6 lattice-protein structures using the Miyazawa-Jernigan (MJ) matrix. The designability of a structure is the number of sequences that design the structure, i.e. sequences that have that…

Protein folds are highly designable, in the sense that many sequences fold to the same conformation. In the present work we derive an expression for the designability in a 20 letter lattice model of proteins which, relying only on the…

We have exactly enumerated all sequences and conformations of HP proteins with chains of up to 19 monomers on the simple cubic lattice. For two variants of the hydrophobic-polar (HP) model, where only two types of monomers are…

The precise sequence of aminoacids plays a central role in the tertiary structure of proteins and their functional properties. The Hydrophobic-Polar lattice models have provided valuable insights regarding the energy landscape. We…

The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states) were enumerated without restrictions on the…

Among an infinite number of possible folds, nature has chosen only about 1000 distinct folds to form protein structures. Theoretical studies suggest that selected folds are intrinsically more designable than others; these selected folds are…

Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…

Using an off-lattice model, we fully enumerate folded conformations of polypeptide chains of up to N = 19 monomers. Structures are found to differ markedly in designability, defined as the number of sequences with that structure as a unique…

Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…

Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…

Simple coarse-grained hydrophobic-polar models for heteropolymers as the lattice HP and the off-lattice AB model allow a general classification of characteristic behaviors for hydrophobic-core based tertiary folding. The strongly reduced…

We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this…

In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…

Here we present an approximate analytical theory for the relationship between a protein structure's contact matrix and the shape of its energy spectrum in amino acid sequence space. We demonstrate a dependence of the number of sequences of…

We study the space of all compact structures on a two-dimensional square lattice of size $N=6\times6$. Each structure is mapped onto a vector in $N$-dimensions according to a hydrophobic model. Previous work has shown that the…

Applying the contact density chain-growth algorithm to lattice heteropolymers, we identify the conformational transitions of a nongrafted hydrophobic-polar heteropolymer with 103 residues in the vicinity of a polar, a hydrophobic, and a…

We present an algorithm for the exhaustive enumeration of all monomer sequences and conformations of short lattice proteins as described by the hydrophobic-polar (HP) model. The algorithm is used for an exact identification of all designing…

We use inverse methods of statistical mechanics to explore trade-offs associated with designing interactions to stabilize self-assembled structures against changes in density or temperature. Specifically, we find isotropic,convex-repulsive…