Crystal structure and Hirshfeld surface analysis of 3-(cyclo-propyl-meth-oxy)-4-(di-fluoro-meth-oxy)-N-(pyridin-2-ylmeth-yl)benzamide.

The title compound, C18H18F2N2O3, crystallizes with two independent mol-ecules (A and B) in the asymmetric unit. They differ essentially in the orientation of the pyridine ring with respect to the benzene ring; these two rings are inclined to each other by 53.3 (2)° in mol-ecule A and by 72.9 (2)° in mol-ecule B. The 3-(cyclo-propyl-meth-oxy) side chain has an extended conformation in both mol-ecules. The two mol-ecules are linked by a pair of C-H⋯O hydrogen bonds and two C-H⋯π inter-actions, forming an A-B unit. In the crystal, this unit is linked by N-H⋯O hydrogen bonds, forming a zigzag -A-B-A-B- chain along [001]. The chains are linked by C-H⋯N and C-H⋯F hydrogen bonds to form layers parallel to the ac plane. Finally, the layers are linked by a third C-H⋯π inter-action, forming a three-dimensional structure. The major contributions to the Hirshfeld surface are those due to H⋯H contacts (39.7%), followed by F⋯H/H⋯F contacts (19.2%).

Crystal structures of disordered Z-type helices.

The X-ray crystal structures of a decamer sequence d(CGCGTACGCG)2 and a tetradecamer sequence d(CGCGCGTACGCGCG)2 are presented here. Both sequences are alternating pyrimidine-purine repeat sequences and they form disordered, pseudo-continuous left handed Z-type helices. They demonstrate interesting variants of the 'bundles of columns of helices' mode of packing.

Protein-small molecule docking with receptor flexibility in iMOLSDOCK.

We have earlier reported the iMOLSDOCK technique to perform 'induced-fit' peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein-ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time. The source code and binary of MOLS 2.0 (under a GNU Lesser General Public License) are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .

[BCIgEPRED-a Dual-Layer Approach for Predicting Linear IgE Epitopes].

Allergy is a common health problem worldwide, especially food allergy. Since B cell epitopes that are recognized by the IgE antibodies act as antigenic determinants for allergy, they play a vital role in diagnostics. Hence, knowledge of an IgE binding epitope in a protein is of particular interest for identifying aller-genic proteins. Though IgE epitopes maybe conformational or linear, identification of the later is useful especially in food allergens that undergo processing or digestion. Very few computational tools are available for the prediction of linear IgE epitopes. Here we report a prediction system that predicts the exact linear IgE epitope. Since our earlier study on linear B cell epitope prediction demonstrated the effectiveness of using an exact epitope dataset (in contrast to epitope containing region datasets), the dataset in this study uses only experimentally verified exact IgE, IgG, IgM and IgA epitopes. Models for Support Vector Machine (SVM) and Random Forest (RF) were constructed adopting Dipeptide Deviation from the Expected mean (DDE) feature vector. Extensive validation procedures including five-fold cross validation and two different independent dataset tests have been performed to validate the proposed method, which achieved a balanced accuracy ranging from 74 to 78% with area under receiver operator curve greater than 0.8. Performance of the proposed method was observed to be better (accuracy difference of 16-28%) in comparison to the existing available method. The proposed method is developed as a standalone tool that could be used for predicting IgE epitopes as well as to be incorporated into any allergen prediction toolhttps://github.com/brsaran/BCIgePred.

iMOLSDOCK: Induced-fit docking using mutually orthogonal Latin squares (MOLS).

We have earlier reported the MOLSDOCK technique to perform rigid receptor/flexible ligand docking. The method uses the MOLS method, developed in our laboratory. In this paper we report iMOLSDOCK, the 'flexible receptor' extension we have carried out to the algorithm MOLSDOCK. iMOLSDOCK uses mutually orthogonal Latin squares (MOLS) to sample the conformation and the docking pose of the ligand and also the flexible residues of the receptor protein. The method then uses a variant of the mean field technique to analyze the sample to arrive at the optimum. We have benchmarked and validated iMOLSDOCK with a dataset of 44 peptide-protein complexes with peptides. We have also compared iMOLSDOCK with other flexible receptor docking tools GOLD v5.2.1 and AutoDock Vina. The results obtained show that the method works better than these two algorithms, though it consumes more computer time.

Comparison of X-ray crystal structures of a tetradecamer sequence d(CCCGGGTACCCGGG)2 at 1.7 Å resolution.

We present here a comparison of three different X-ray crystal structures of DNA tetradecamer sequence d(CCCGGGTACCCGGG)2 all at about 1.7 Å resolution. The sequence was designed as an attempt to form a DNA four-way junction with A-type helical arms. However, in the presence of zinc, magnesium, and in the absence of any metal ion, it does not take up the junction structure, but forms an A-type double helix. This allowed us to study possible conformational changes in the double helix due to the presence of metal ions. Upon addition of the zinc ion, there is a change in the space group from P41212 to P41. The overall conformation of the duplex remains the same. There are small changes in the interaction of the metal ions with the DNA. In the zinc-bound structure, there are two zinc ions that show direct interaction with the N7 atoms of terminal G13 bases at either end of the molecule. There are small changes in the interhelical contacts. The consequence of these differences is to break some of the symmetry and change the space group.

MOLS 2.0: software package for peptide modeling and protein-ligand docking.

We previously developed an algorithm to perform conformational searches of proteins and peptides, and to perform the docking of ligands to protein receptors. In order to identify optimal conformations and docked poses, this algorithm uses mutually orthogonal Latin squares (MOLS) to rationally sample the vast conformational (or docking) space, and then analyzes this relatively small sample using a variant of mean field theory. The conformational search part of the algorithm was denoted MOLS 1.0. The docking portion of the algorithm, which allows only "flexible ligand/rigid receptor" docking, was denoted MOLSDOCK. Both are FORTRAN-based command-line-only molecular docking computer programs, though a GUI was developed later for MOLS 1.0. Both the conformational search and the rigid receptor docking parts of the algorithm have been extensively validated. We have now further enhanced the capabilities of the program by incorporating "induced fit" side-chain receptor flexibility for docking peptide ligands. Benchmarking and extensive testing is now being carried out for the flexible receptor portion of the docking. Additionally, to make both the peptide conformational search and docking algorithms (the latter including both flexible ligand/rigid receptor and flexible ligand/flexible receptor techniques) more accessible to the research community, we have developed MOLS 2.0, which incorporates a new Java-based graphical user interface (GUI). Here, we give a detailed description of MOLS 2.0. The source code and binary for MOLS 2.0 are distributed free (under a GNU Lesser General Public License) to the scientific community. They are freely available for download at https://sourceforge.net/projects/mols2-0/files/ .

Restricted mobility of side chains on concave surfaces of solenoid proteins may impart heightened potential for intermolecular interactions.

Significant progress has been made in the determination of the protein structures with their number today passing over a hundred thousand structures. The next challenge is the understanding and prediction of protein-protein and protein-ligand interactions. In this work we address this problem by analyzing curved solenoid proteins. Many of these proteins are considered as "hub molecules" for their high potential to interact with many different molecules and to be a scaffold for multisubunit protein machineries. Our analysis of these structures through molecular dynamics simulations reveals that the mobility of the side-chains on the concave surfaces of the solenoids is lower than on the convex ones. This result provides an explanation to the observed preferential binding of the ligands, including small and flexible ligands, to the concave surface of the curved solenoid proteins. The relationship between the landscapes and dynamic properties of the protein surfaces can be further generalized to the other types of protein structures and eventually used in the computer algorithms, allowing prediction of protein-ligand interactions by analysis of protein surfaces.

Interactions of Mn2+ with a non-self-complementary Z-type DNA duplex.

Crystal structures of the hexanucleotide d(CACGCG)·d(CGCGTG) were determined in two crystal lattices when different concentrations of the counterion Mn2+ were used in crystallization. The availability of Mn2+ during the crystallization process appears to play an important role in inducing different crystal packings that lead to crystals belonging to the two space groups P2(1) and P6(5). Analysis of the molecular interactions of Mn2+ with the Z-form duplexes shows direct coordination to the purine residues G and A.

Crystallographic and spectroscopic studies of d(CCGGTACCGG).

The decanucleotide sequence d(CCGGTACCGG) crystallizes as a four-way junction at low cobalt ion concentrations (i.e., 1 mM). When the cobalt concentration in the crystallization solution is increased to 5 mM, the sequence crystallizes as resolved B-DNA duplexes. Gel retardation studies of the decamer show both a faint slow-moving band and a much thicker fast-moving band at low cobalt ion concentrations, and only the intense fast-moving band at higher ion concentration. Circular dichroism (CD) spectroscopy of the decamer indicates a structural transition as the cobalt ion concentration in the solution is increased, probably from B-type to A-type DNA. These studies revealed that the oligomer sequence has several conformations and structures accessible to it, in a manner dependent on sequence, ion concentration, and DNA concentration. [Supplementary materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides & Nucleic Acids for the following free supplemental resources(s): Supplementary Figures 1, 2, and 3.].

Conformational space exploration of Met- and Leu-enkephalin using the MOLS method, molecular dynamics, and Monte Carlo simulation--a comparative study.

We report here a comparative study of the molecular conformational energy landscape generated using the mutually orthogonal Latin squares (MOLS) method, molecular dynamics (MD), and Monte Carlo (MC) simulation. The MOLS method, as described earlier from our laboratory, uses an experimental design technique to rapidly and exhaustively sample the low energy conformations of a molecule. MD and MC simulations have been used to perform similar tasks. In the comparison reported here, the three methods were applied to a pair of neuropeptides, namely Met- and Leu-enkephalin. A set of 1500 conformations of these enkephalins were generated using these methods with CHARMM22 force field, and the resulting samples were analyzed to determine the extent and nature of coverage of the conformational space. The results indicate that the MOLS method samples a larger number of possible conformations and identifies conformations closer to the experimental structures than the MD and MC simulations.

Structure of d(CGGGTACCCG)4 as a four-way Holliday junction.

The crystal structure of the decamer sequence d(CGGGTACCCG)(4) as a four-way Holliday junction has been determined at 2.35 Å resolution. The sequence was designed in order to understand the principles that govern the relationship between sequence and branching structure. It crystallized as a four-way junction structure with an overall geometry similar to those of previously determined Holliday junction structures.

Age, co-morbidity and poor mobility: no evidence of predicting in-patient death and acute hospital length of stay in the oldest old.

BACKGROUND: The oldest old (aged over 90 years) are the fastest growing section of the UK population. Limited data exist regarding the effect of age, location, co-morbidity and physical performance status on outcome of acute illness in this age group. METHODS: We performed a prospective study in people aged ≥ 90 years using hospital audit data in three hospitals in England and Scotland. We examined the characteristics of those admitted over three consecutive calendar months and calculated risk ratios of death and prolonged length of acute hospital stay (>7 days). RESULTS: A total of 419 patients were included in this study (68% female, median age 93 years). There were similarities in presentation and diagnoses, but patients in Scotland (n = 164) were more likely to be admitted from sheltered housing or nursing homes than those in England (n = 255). Patients in England were significantly less likely to be able to mobilize < 10 m (41 vs. 34%, P < 0.001) but had lower prevalence of hypertension (40 vs. 55%, P = 0.02), ischaemic heart disease (30% vs. 45%, P = 0.02) and fewer prescribed medications (median 2 vs. 3, P < 0.001). Mortality was similar for the England and Scotland centres (P = 0.98). Previously recognized risk factors for death following hospital admission and length of stay e.g. older age, higher number of co-morbidities and poor mobility were not predictive in this study. CONCLUSION: The 'oldest old' should not be considered as a homogenous group and findings from single-centre studies involving this age group may not be generalizable. We found no conclusive evidence that patient-related factors predict outcome in this age group in acute medical admission settings.

The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)2.

We report the 2.6Å resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P43. This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours.

The sequence d(CGGCGGCCGC) self-assembles into a two dimensional rhombic DNA lattice.

We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind to each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5Å. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.

Protein-ligand docking using mutually orthogonal Latin squares (MOLSDOCK).

The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We have proposed a docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to search through both the conformational space of a peptide as well its docking space. Here we extend this method to simultaneously identify both the low energy conformation as well as a high scoring docking mode for the small organic ligand molecules. Application of the method to 45 protein-ligand complexes, in which the number of rotatable torsions varies from 2 to 19, and comparisons with AutoDock 4.0, showed that the method works well.

The structure of d(CACACG).d(CGTGTG).

The crystal structure of d(CACACG).d(CGTGTG) was solved to a resolution of 2.05 A in space group P2(1). The duplex assumes the left-handed Z-DNA structure. The presence of two A.T base pairs in the hexamer does not greatly affect the conformation. The most significant changes compared with the regular structure of Z-DNA are in the values of twist in the central portion of the helix. This variation, as well as others in the values of roll, inclination etc., follow the pattern observed previously in the structure of d(CGCACG).d(CGTGCG).

Effects of Hydration on the Conformational Energy Landscape of the Pentapeptide Met-Enkephalin.

We report here a study of the conformational energy landscape of the pentapeptide Met-enkephalin in the presence of explicit solvent (water) molecules. A sample of 1 500 low-energy structures of this molecule was generated using the mutually orthogonal Latin squares (MOLS) technique with the CHARMM22 force field. This technique, developed in our laboratory, allows us to sample the conformational space of a molecule in an unbiased and exhaustive manner. The study shows that inclusion of explicit solvation is important to correctly model the conformational behavior of the molecule. Structures modeled in the presence of water molecules are far more similar to the experimental structures than when the water molecules are excluded. The results also indicate that the pentapeptide Met-enkephalin prefers extended structures in an aqueous environment, as against tightly folded structures in the absence of water. Thus, the biologically relevant structure, when the molecule is not bound to the receptor, is probably the extended structure, as seen in the crystallographic and NMR experiments, rather than the GEM structures calculated by various workers.

A new peptide docking strategy using a mean field technique with mutually orthogonal Latin square sampling.

The theoretical prediction of the association of a flexible ligand with a protein receptor requires efficient sampling of the conformational space of the ligand. Several docking methodologies are currently available. We propose a new docking technique that performs well at low computational cost. The method uses mutually orthogonal Latin squares to efficiently sample the docking space. A variant of the mean field technique is used to analyze this sample to arrive at the optimum. The method has been previously applied to explore the conformational space of peptides and identify structures with low values for the potential energy. Here we extend this method to simultaneously identify both the low energy conformation as well as a 'high-scoring' docking mode. Application of the method to 56 protein-peptide complexes, in which the length of the peptide ligand ranges from three to seven residues, and comparisons with Autodock 3.05, showed that the method works well.

Hydrophobic clusters in protein structures.

Globular proteins fold such that the hydrophobic groups are packed inside forming hydrophobic clusters, and the hydrophilic groups are present on the surface. In this article we analyze clusters of hydrophobic groups of atoms in 781 protein structures selected from the PDB. Our analysis showed that every structure consists of two types of clusters: at least one large cluster that forms the hydrophobic core and probably dictates the protein fold; and numerous smaller clusters, which might be involved in the stabilization of the fold. We also analyzed the preference of the hydrophobic groups in each of the amino acids toward forming hydrophobic clusters. We find that hydrophobic groups from the hydrophilic amino acids also contribute toward cluster formation.