3,339 research outputs found
Statistical Geometry of Packing Defects of Lattice Chain Polymer from Enumeration and Sequential Monte Carlo Method
Voids exist in proteins as packing defects and are often associated with
protein functions. We study the statistical geometry of voids in
two-dimensional lattice chain polymers. We define voids as topological features
and develop a simple algorithm for their detection. For short chains, void
geometry is examined by enumerating all conformations. For long chains, the
space of void geometry is explored using sequential Monte Carlo importance
sampling and resampling techniques. We characterize the relationship of
geometric properties of voids with chain length, including probability of void
formation, expected number of voids, void size, and wall size of voids. We
formalize the concept of packing density for lattice polymers, and further
study the relationship between packing density and compactness, two parameters
frequently used to describe protein packing. We find that both fully extended
and maximally compact polymers have the highest packing density, but polymers
with intermediate compactness have low packing density. To study the
conformational entropic effects of void formation, we characterize the
conformation reduction factor of void formation and found that there are strong
end-effect. Voids are more likely to form at the chain end. The critical
exponent of end-effect is twice as large as that of self-contacting loop
formation when existence of voids is not required. We also briefly discuss the
sequential Monte Carlo sampling and resampling techniques used in this study.Comment: 29 pages, including 12 figure
NMR shieldings from density functional perturbation theory: GIPAW versus all-electron calculations
We present a benchmark of the density functional linear response calculation
of NMR shieldings within the Gauge-Including Projector-Augmented-Wave method
against all-electron Augmented-Plane-Wavelocal-orbital and uncontracted
Gaussian basis set results for NMR shieldings in molecular and solid state
systems. In general, excellent agreement between the aforementioned methods is
obtained. Scalar relativistic effects are shown to be quite large for nuclei in
molecules in the deshielded limit. The small component makes up a substantial
part of the relativistic corrections.Comment: 3 figures, supplementary material include
A Two-Coordinate Nickel Imido Complex That Effects C−H Amination
An exceptionally low coordinate nickel imido complex, (IPr*)Ni═N(dmp) (2) (dmp = 2,6-dimesitylphenyl), has been prepared by the elimination of N_2 from a bulky aryl azide in its reaction with (IPr*)Ni(η^6-C_7H_8) (1). The solid-state structure of 2 features two-coordinate nickel with a linear C−Ni−N core and a short Ni−N distance, both indicative of multiple-bond character. Computational studies using density functional theory showed a Ni═N bond dominated by Ni(dπ)−N(pπ) interactions, resulting in two nearly degenerate singly occupied molecular orbitals (SOMOs) that are Ni−N π* in character. Reaction of 2 with CO resulted in nitrene-group transfer to form (dmp)NCO and (IPr*)Ni(CO)_3 (3). Net C−H insertion was observed in the reaction of 2 with ethene, forming the vinylamine (dmp)NH(CH═CH_2) (5) via an azanickelacyclobutane intermediate, (IPr*)Ni{N,C:κ^2-N(dmp)CH_2CH_2} (4)
Magnetic groundstate and Fermi surface of bcc Eu
Using spin-spiral technique within the full potential linearized
augmented-plane-waves (LAPW) electronic structure method we investigate the
magnon spectrum and N\'eel temperature of bcc Eu. Ground state corresponding to
an incommensurate spin-spiral is obtained in agreement with experiment and
previous calculations. We demonstrate that the magnetic coupling is primarily
through the intra-atomic and exchange and
Ruderman-Kittel-Kasuya-Yosida mechanism. We show that the existence of this
spin-spiral is closely connected to a nesting feature of the Fermi surface
which was not noticed before.Comment: 6 pages 8 figure
PocketMatch: A new algorithm to compare binding sites in protein structures
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented
Do all pure entangled states violate Bell's inequalities for correlation functions?
Any pure entangled state of two particles violates a Bell inequality for
two-particle correlation functions (Gisin's theorem). We show that there exist
pure entangled N>2 qubit states that do not violate any Bell inequality for N
particle correlation functions for experiments involving two dichotomic
observables per local measuring station. We also find that
Mermin-Ardehali-Belinskii-Klyshko inequalities may not always be optimal for
refutation of local realistic description.Comment: 4 pages, journal versio
FLORA: a novel method to predict protein function from structure in diverse superfamilies
Predicting protein function from structure remains an active area of interest, particularly for the structural genomics initiatives where a substantial number of structures are initially solved with little or no functional characterisation. Although global structure comparison methods can be used to transfer functional annotations, the relationship between fold and function is complex, particularly in functionally diverse superfamilies that have evolved through different secondary structure embellishments to a common structural core. The majority of prediction algorithms employ local templates built on known or predicted functional residues. Here, we present a novel method (FLORA) that automatically generates structural motifs associated with different functional sub-families (FSGs) within functionally diverse domain superfamilies. Templates are created purely on the basis of their specificity for a given FSG, and the method makes no prior prediction of functional sites, nor assumes specific physico-chemical properties of residues. FLORA is able to accurately discriminate between homologous domains with different functions and substantially outperforms (a 2–3 fold increase in coverage at low error rates) popular structure comparison methods and a leading function prediction method. We benchmark FLORA on a large data set of enzyme superfamilies from all three major protein classes (α, β, αβ) and demonstrate the functional relevance of the motifs it identifies. We also provide novel predictions of enzymatic activity for a large number of structures solved by the Protein Structure Initiative. Overall, we show that FLORA is able to effectively detect functionally similar protein domain structures by purely using patterns of structural conservation of all residues
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