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

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)

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-Wave$+$local-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

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 $f-s$ and $f-d$ 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

Molecular basis of FIR-mediated c-myc transcriptional control

The far upstream element (FUSE) regulatory system promotes a peak in the concentration of c-Myc during cell cycle. First, the FBP transcriptional activator binds to the FUSE DNA element upstream of the c-myc promoter. Then, FBP recruits its specific repressor (FIR), which acts as an on/off transcriptional switch. Here we describe the molecular basis of FIR recruitment, showing that the tandem RNA recognition motifs of FIR provide a platform for independent FUSE DNA and FBP protein binding and explaining the structural basis of the reversibility of the FBP-FIR interaction. We also show that the physical coupling between FBP and FIR is modulated by a flexible linker positioned sequentially to the recruiting element. Our data explain how the FUSE system precisely regulates c-myc transcription and suggest that a small change in FBP-FIR affinity leads to a substantial effect on c-Myc concentration.MRC Grant-in-aid U11757455

Structural and functional characterization of Pseudomonas aeruginosa CupB chaperones

Pseudomonas aeruginosa, an important human pathogen, is estimated to be responsible for,10% of nosocomial infections worldwide. The pathogenesis of P. aeruginosa starts from its colonization in the damaged tissue or medical devices (e. g. catheters, prothesis and implanted heart valve etc.) facilitated by several extracellular adhesive factors including fimbrial pili. Several clusters containing fimbrial genes have been previously identified on the P. aeruginosa chromosome and named cup [1]. The assembly of the CupB pili is thought to be coordinated by two chaperones, CupB2 and CupB4. However, due to the lack of structural and biochemical data, their chaperone activities remain speculative. In this study, we report the 2.5 A crystal structure of P. aeruginosa CupB2. Based on the structure, we further tested the binding specificity of CupB2 and CupB4 towards CupB1 (the presumed major pilus subunit) and CupB6 (the putative adhesin) using limited trypsin digestion and strep-tactin pull-down assay. The structural and biochemical data suggest that CupB2 and CupB4 might play different, but not redundant, roles in CupB secretion. CupB2 is likely to be the chaperone of CupB1, and CupB4 could be the chaperone of CupB4:CupB5:CupB6, in which the interaction of CupB4 and CupB6 might be mediated via CupB5