Geometrically Reduced Number of Protein Ground State Candidates

Geometrical properties of protein ground states are studied using an algebraic approach. It is shown that independent from inter-monomer interactions, the collection of ground state candidates for any folded protein is unexpectedly small: For the case of a two-parameter Hydrophobic-Polar lattice model for $L$-mers, the number of these candidates grows only as $L^2$. Moreover, the space of the interaction parameters of the model breaks up into well-defined domains, each corresponding to one ground state candidate, which are separated by sharp boundaries. In addition, by exact enumeration, we show there are some sequences which have one absolute unique native state. These absolute ground states have perfect stability against change of inter-monomer interaction potential.Comment: 9 page, 4 ps figures are include

Extreme bendability of DNA double helix due to bending asymmetry

Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study (B. Eslami-Mossallam and M. Ejtehadi, Phys. Rev. E 80, 011919 (2009)). Exploiting a coarse grained representation of DNA molecule at base pair (bp) level, and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that, for DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.Comment: 8 pages, 9 figure

Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions

We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically non-degenerate vectors (structures) as protein-like structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of designability-ranking shows that about 1/e of the structures have designabilities above the average, independent on the used model.Comment: 17 pages and 10 figure

Plant Diversity Patterns Along Altitudinal Gradient in Understory Communities of Darkesh Region, Bojnord, Iran

The ecotone region of Darkesh with an area of 22,500 hectares is located in the Irano-Turanian xeric-continental bioclimatic zone of Khorassan-Kopet Dagh. To investigate the plant diversity patterns of understory communities along three elevation classes of 1100-1600, 1600-2100, and 2100-2600 m, 187 plots were sampled randomly and abundance and cover of species were recorded using 4-m2 plots. Beta diversity and Hill indices were calculated by using R and PAST software. A total of 252 species were recorded including 31 perennial grasses. The most abundant grasses were Poa nemoralis, Poa bulbosa, Bromus sterilis, Brachypodium sylvaticum, and Dactylis glomerata subsp. glomerata. Poa nemoralis was an important dominant grass under Quercus community. From the standpoint of species richness, Hill indices were highest under woods stories along the elevation of 1100-1600 m. Understories of oak forest and alpine communities had almost the same indices and were in the second rank compared to woods communities. Based on the β diversity index, the wood understory had the highest indices followed by Quercus and alpine communities. By increasing the elevations, the diversity of understory communities also decreased

Species diversity and ecological studies of phytoplankton in the Bazangan Lake

Bazangan, the Khorasan largest natural lake, is located in Northeast. 120km from Mashhad with the area of 690000m2. The purpose of this study was to characterize ecological aspects and to compare seasonal variations in species diversity of phytoplanktons in the surface water of littoral zone in the Bazangan lake. Samples were collected from eleven stations in each season during the year 2002. Some ecological factors such as pH. EC, salinity, hardness of water, nutrients and water temperature were measured. Four macroalgae and 33 phytoplankton species belonging to 5 algae groups viz. Chrysophyta (21 species). Chlorophyta (7 species), Cyanophyta (4 species) and Pyrrophyta (1 species) were identified. Diatoma tennis. Fragillaria crotonensis, Lilothrix subtilissinia and Merisinopodia punctata had the most species abundance. Comparing to other groups, Chrysophyta was abundant in all seasons mostly in the spring and summer. Different numerical indices of diversity such as species richness, evenness and diversity as well as parametric families of diversity were obtained in different seasons based on the abundance data of phytoplanktons. The results showed that the highest species diversity of the phytoplanktons could be seen in the summer and autumn. The Bazangan is classified as an oligothroph and a subsaline lake

Synopsis of the genus Alyssum in Iran

A complete, up to date checklist of Alyssum species reported from Iran is presented in this review. The distribution of these species was considered in Iran and in the adjacent countries, too. Additional records were obtained from Flora Iranica, Flora of Turkey and other references. In Iran some species (e. g., Alyssum hezarmasjedensis, A. mozaffarianii, A. persicum, A. polycladum, A. stipitatum, A. turgidum) have very restricted distribution. Iran is the second important locality for the following species: A. anatolicum, A. contemptum, A. filiforme, A. iranicum, A. lycaonicum, A. niveum, A. penjwinense. The other Alyssum species are widespread in Iran and in the adjacent countries

The Origin of the Designability of Protein 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. Second, whether the structure of the used lattice is bipartite or not. Third, the effect of the length of the chain, namely, the number of monomers on the chain. We found that the bipartiteness of the lattice structure is not a main factor which determines the designability. Our results suggest that highly designable structures will be found when the length of the chain is sufficiently long to make the hydrophobic core consisting of enough number of monomers.Comment: 17 pages, 2 figure

Highly Designable Protein Structures and Inter Monomer Interactions

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 interaction potential becomes larger than a critical value, the degree of designability of structures will depend on the parameters of potential. We also show that the existence of a unique ground state is highly sensitive to mutation in certain sites.Comment: 14 pages, Latex file, 3 latex and 6 eps figures are include

Statistical properties of contact vectors

We study the statistical properties of contact vectors, a construct to characterize a protein's structure. The contact vector of an N-residue protein is a list of N integers n_i, representing the number of residues in contact with residue i. We study analytically (at mean-field level) and numerically the amount of structural information contained in a contact vector. Analytical calculations reveal that a large variance in the contact numbers reduces the degeneracy of the mapping between contact vectors and structures. Exact enumeration for lengths up to N=16 on the three dimensional cubic lattice indicates that the growth rate of number of contact vectors as a function of N is only 3% less than that for contact maps. In particular, for compact structures we present numerical evidence that, practically, each contact vector corresponds to only a handful of structures. We discuss how this information can be used for better structure prediction.Comment: 20 pages, 6 figure

An Analytical Approach to the Protein Designability Problem

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 spectrum, the designability of a structure can be estimated. We outline a heirarchy of structures, from most to least designable, and show that this heirarchy depends on the potential that is used.Comment: 16 pages 4 figure