相关论文: Highly Designable Protein Structures and Inter Mon…

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…

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…

The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…

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 enumerating all sequences of length 20, we study the designability of structures in a two-dimensional Hydrophobic-Polar (HP) lattice model in a wide range of inter-monomer interaction parameters. We find that although the histogram of…

We present the results of a self-consistent, unified molecular dynamics study of simple model heteropolymers in the continuum with emphasis on folding, sequence design and the determination of the interaction parameters of the effective…

Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…

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…

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…

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…

It is widely accepted that (1) the natural or folded state of proteins is a global energy minimum, and (2) in most cases proteins fold to a unique state determined by their amino acid sequence. The H-P (hydrophobic-hydrophilic) model is a…

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…

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…

We review the recent progress in computational approaches to protein design which builds on advances in statistical-mechanical protein folding theory. In particular, we evaluate the degeneracy of the protein code (i.e. how many sequences…

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…

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…

On the study of protein folding, our understanding about the protein structures is limited. In this paper we find one way to characterize the compact structures of lattice protein model. A quantity called Partnum is given to each compact…

Protein structures are a very special class among all possible structures. It was suggested that a ``designability principle'' plays a crucial role in nature's selection of protein sequences and structures. Here we provide a theoretical…

We study a simple heteropolymer model containing sequence-independent local interactions on both square and triangular lattices. Sticking to a two-letter code, we investigate the model for varying strength $\kappa$ of the local…

Protein sequences are believed to have been selected to provide the stability of, and reliable renaturation to, an encoded unique spatial fold. In recently proposed theoretical schemes, this selection is modeled as ``minimal frustration,''…