Separation, folding and shearing of graphene layers during wedge-based mechanical exfoliation.

We report, using molecular dynamics simulation studies, how and under what conditions graphene layers separate, fold and shear during a wedge-based mechanical exfoliation machining technique to produce few-layer graphene. Our previously reported experimental results using this novel technique have shown clear evidence of few-layer graphene being subjected to such phenomena. Molecular simulations of initial wedge engagement show that the entry location of the wedge tip vis-á-vis the nearest graphene layer plays a key role in determining whether layers separate or fold and which layers and how many of them fold. We also show that depending on this entry location several successive layers beneath the wedge undergo significant elastic bending, consuming energies requiring large vertical forces to be imposed by the moving wedge. The layer separation force itself is seen to be minimal and consistent with breaking up of van der Waals interactions. In addition, shearing of layers occurs mainly during wedge exit and depends largely on the wedge speed and also its depth of insertion. Understanding the conditions at which this separation, folding and shearing of the graphene layers takes place, one can control or tune the wedge-based exfoliation technique for particular kinds of graphene layers.

Low-resolution real-space envelopes: an approach to the ab initio macromolecular phase problem.

An ab initio approach to the phase problem in macromolecular x-ray crystallography is described. A random gas of hard-sphere point scatterers is allowed to condense under the constraint of the solvent fraction and the restraint of the observed Fourier amplitude data. Two applications to real macromolecular examples are discussed. This method produces an approximate outline of the bulk solvent regions and thus yields a low-resolution picture of the unit cell that can be extended to higher resolutions in special cases, such as through the use of molecular replacement or of noncrystallographic symmetry-based phase extension.

Autologous graft-versus-host disease: harnessing anti-tumor immunity through impaired self-tolerance.

The absence of a graft-versus-malignancy (GVM) effect may be responsible for the higher relapse rate seen after autologous hematopoietic cell transplantation (auto-HCT) compared with allogeneic hematopoietic cell transplantation (allo-HCT). Acute GVHD developing after allo-HCT, however, is associated with significant morbidity and mortality. An autoimmune syndrome similar to acute GVHD has been reported to occur after auto-HCT and has been termed the 'auto-aggression' syndrome or autologous GVHD (auto-GVHD). Auto-GVHD tends to be milder than classical GVHD, most commonly involves the skin (rarely the gastrointestinal tract, liver or both) and often is self-limited. Auto-GVHD has been reported to occur both spontaneously and in subjects receiving post transplant immune modulation with CsA, IFN-gamma or the combination. The development of auto-GVHD depends upon the derangement of self tolerance either through administration of post transplant CsA, depletion of regulatory T cells following the preparative chemoradiotherapy or both. Self-reactive CD8(+) T cells paradoxically are able to recognize a self peptide antigen presented by MHC class II molecules and appear to mediate the syndrome. Many clinical trials have been performed using CsA with or without IFN-gamma in an attempt to induce auto-GVHD. While many patients do indeed develop the syndrome, any associated anti-tumor effect remains questionable to date. New strategies to exploit auto-GVHD and enhance a GVM effect such as through the depletion of regulatory T cells or through use of newer immunomodulatory agents may improve the efficacy of auto-HCT.

Anaplastic Carcinoma Thyroid - A Review on the Management of this Aggressive Cancer.

Anaplastic carcinoma thyroid is an aggressive malignancy with very poor survival rate. In this study, we reviewed the records of 34 patients with anaplastic carcinoma thyroid in our centre and we divided them into groups T4a, T4b, and T4c. The case records were reviewed for presentation, diagnosis, treatment and follow-up and we analysed the data using statistical methods. The median age group was 65 years with 22 women and 12 men. There were 16 patients (47%) with a history of thyroid swelling of more than 2 years duration. Of these 16 patients 6 were found to be in T4a group. There were 6 patients in T4a, 14 each in T4b and T4c. All the patients in T4a group were operated and completed multimodal management. The group with T4a had the best prognosis with a mean survival of 1 year. The patients with extracapsular disease (T4b) completed chemotherapy along with radiotherapy. These patients had a mean survival of 6 months. Only 2 patients in metastatic group completed the course of chemotherapy with radiotherapy. The other 12 patients died during the course of treatment due to respiratory failure. The mean survival in this group was a dismal 15 days. On univariate analysis metastatic disease, extracapsular disease, size more than 5 cm and involvement of lymph nodes were the reasons for incomplete treatment and hence markers of worst prognosis. There are 47% of the patients with prior history of thyroid swelling which gives us time to identify and manage thyroid swellings with propensity to undergo anaplastic transformation.

Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core.

BACKGROUND: In recent years, the determination of large numbers of protein structures has created a need for automatic and objective methods for the comparison of structures or conformations. Many protein structures show similarities of conformation that are undetectable by comparing their sequences. Comparison of structures can reveal similarities between proteins thought to be unrelated, providing new insight into the interrelationships of sequence, structure and function. RESULTS: Using a new tool that we have developed to perform rapid structural alignment, we present the highlights of an exhaustive comparison of all pairs of protein structures in the Brookhaven protein database. Notably, we find that the DNA-binding domain of the bacteriophage repressor family is almost completely embedded in the larger eight-helix fold of the globin family of proteins. The significant match of specific residues is correlated with functional, structural and evolutionary information. CONCLUSION: Our method can help to identify structurally similar folds rapidly and with high-sensitivity, providing a powerful tool for analyzing the ever-increasing number of protein structures being elucidated.

Automatic and accurate method for analysis of proteins that undergo hinge-mediated domain and loop movements.

BACKGROUND: The structures of proteins that undergo significant main-chain conformational change are reported with increasing frequency. Three-dimensional atomic models are often available for two alternative conformational states of the same molecule. Inspection has shown these states to be varied in nature, arising by mechanisms that include hinge-facilitated closure between domains and smaller-scale loop motions within domains; these movements are often induced by metal ion binding or ligand binding. Polypeptides that display flexible segments are also observed in different crystal conformations or as alternatively packed subunits. Although subjective visual inspection has been previously used to compare structures and analyze conformational changes, there is a need for an objective method. RESULTS: We have developed a straightforward, robust, and objective algorithm that can locate the residues that mediate and participate in the changes between the two conformational states. Our method does not require initial superpositioning. We illustrate the method by considering several test cases. The first example is maltose binding protein, a polypeptide that exhibits rigid-body domain closure involving multiple hinges. The second is lactate dehydrogenase, which undergoes both loop and subdomain movement; we accurately describe the location and relative magnitude of these deformations. Finally, in the example of aspartate transcarbamoylase, both hinge-mediated domain movement and functionally relevant loop rearrangements are described. In the instances in which domain closure occurs, the residues that serve as hinges between the domains involved are accurately predicted. In addition, our technique successfully identifies the exact residues that undergo intra-domain loop movements, even for movements that are accompanied by larger scale inter-domain rearrangements. CONCLUSIONS: Our algorithm is successful in its comprehensive analysis and description of complex hinge-mediated domain motion for all structures displaying rigid-body movement and is accurate in identifying the location of any independent intra-domain rearrangements.

A structural explanation for the twilight zone of protein sequence homology.

Homology modeling of protein structures as a function of sequence breaks down at the twilight zone limit of sequence identity between the template and target proteins. Our results suggest that protein sequences that have diverged from a common ancestor beyond the twilight zone may adopt side-chain interactions that are very different from those endowed by the ancestral sequence.

Are coiled-coil proteins evolutionarily related?

A modification to the standard Needleman-Wunsch sequence comparison scheme is presented. In cases where high levels of sequence similarity may arise from a common structural motif, this method discriminates between common ancestry and similarity due to structural constraints alone. Use of this algorithm is illustrated with the coiled-coil motif in the cases of idealized coiled-coil sequences, intermediate filaments and reovirus hemagluttinin.

Prediction of protein side-chain conformation by packing optimization.

We have developed a rapid and completely automatic method for prediction of protein side-chain conformation, applying the simulated annealing algorithm to optimization of side-chain packing (van der Waals) interactions. The method directly attacks the combinatorial problem of simultaneously predicting many residues' conformation, solving in 8 to 12 hours problems for which the systematic search would require over 10(300) central processing unit years. Over a test set of nine proteins ranging in size from 46 to 323 residues, the program's predictions for side-chain atoms had a root-mean-square (r.m.s.) deviation of 1.77 A overall versus the native structures. More importantly, the predictions for core residues were especially accurate, with an r.m.s. value of 1.25 A overall: 80 to 90% of the large hydrophobic side-chains dominating the internal core were correctly predicted, versus 30 to 40% for most current methods. The predictions' main errors were in surface residues poorly constrained by packing and small residues with greater steric freedom and hydrogen bonding interactions, which were not included in the program's potential function. van der Waals interactions appear to be the supreme determinant of the arrangement of side-chains in the core, enforcing a unique allowed packing that in every case so far examined matches the native structure.

A method for multiple sequence alignment with gaps.

A method that performs multiple sequence alignment by cyclical use of the standard pairwise Needleman-Wunsch algorithm is presented. The required central processor unit time is of the same order of magnitude as the standard Needleman-Wunsch pairwise implementation. Comparison with the one known case where the optimal multiple sequence alignment has been rigorously determined shows that in practice the proposed method finds the mathematically optimal solution. The more interesting question of the biological usefulness of such multiple sequence alignment over pairwise approaches is assessed using protein families whose X-ray structures are known. The two such cases studied, the subdomains of the ricin B-chain and the S-domains of virus coat proteins, have low pairwise similarity and thus fail to align correctly under standard pairwise sequence comparison. In both cases the multiple sequence alignment produced by the proposed technique, apart from minor deviations at loop regions, correctly predicts the true structural alignment. Thus, given many sequences of low pairwise similarity, the proposed multiple sequence method, can extract any familial similarity and so produce a sequence alignment consistent with the underlying structural homology.

Recognizing native folds by the arrangement of hydrophobic and polar residues.

Central to the ab initio protein folding problem is the development of an energy function for which the correct native structure has a lower energy than all other conformations. Existing potentials of mean force typically rely extensively on database-derived contact frequencies or knowledge of three-dimensional structural information in order to be successful in the problem of recognizing the native fold for a given sequence from a set of decoy backbone conformations. Is the detailed statistical information or sophisticated analysis used by these knowledge-based potentials needed to achieve the observed degree of success in fold recognition? Here we introduce a novel pairwise energy function that enumerates contacts between hydrophobic residues while weighting their sum by the total number of residues surrounding these hydrophobic residues. Thus it effectively selects compact folds with the desired structural feature of a buried, intact core. This approach represents an advance over using pairwise terms whose energies of interaction that are independent of the position in the protein and greatly improves the discrimination capability of an energy function. Our results show that 85% of a set of 195 representative native folds were recognized correctly. The 29 exceptions were lipophilic proteins, small proteins with prosthetic groups or disulfide bonds, and oligomeric proteins. Overall, our method separates the native fold from incorrect folds by a larger margin (measured in standard deviation units) than has been previously demonstrated by more sophisticated methods. The arrangement of hydrophobic and polar residues alone as evaluated by our novel scoring scheme, is unexpectedly effective at recognizing native folds in general. It is surprising that a simple binary pattern of hydrophobic and polar residues apparently selects a give unique fold topology.

Using a hydrophobic contact potential to evaluate native and near-native folds generated by molecular dynamics simulations.

There are several knowledge-based energy functions that can distinguish the native fold from a pool of grossly misfolded decoys for a given sequence of amino acids. These decoys, which are typically generated by mounting, or "threading", the sequence onto the backbones of unrelated protein structures, tend to be non-compact and quite different from the native structure: the root-mean-squared (RMS) deviations from the native are commonly in the range of 15 to 20 angstroms. Effective energy functions should also demonstrate a similar recognition capability when presented with compact decoys that depart only slightly in conformation from the correct structure (i.e. those with RMS deviations of approximately 5 angstroms or less). Recently, we developed a simple yet powerful method for native fold recognition based on the tendency for native folds to form hydrophobic cores. Our energy measure, which we call the hydrophobic fitness score, is challenged to recognize the native fold from 2000 near-native structures generated for each of five small monomeric proteins. First, 1000 conformations for each protein were generated by molecular dynamics simulation at room temperature. The average RMS deviation of this set of 5000 was 1.5 angstroms. A total of 323 decoys had energies lower than native; however, none of these had RMS deviations greater than 2 angstroms. Another 1000 structures were generated for each at high temperature, in which a greater range of conformational space was explored (4.3 angstroms RMS deviation). Out of this set, only seven decoys were misrecognized. The hydrophobic fitness energy of a conformation is strongly dependent upon the RMS deviation. On average our potential yields energy values which are lowest for the population of structures generated at room temperature, intermediate for those produced at high temperature and highest for those constructed by threading methods. In general, the lowest energy decoy conformations have backbones very close to native structure. The possible utility of our method for screening backbone candidates for the purpose of modelling by side-chain packing optimization is discussed.

Structure of the amino-terminal domain of phage 434 repressor at 2.0 A resolution.

The crystal structure of the amino-terminal domain of phage 434 repressor has been solved using molecular replacement methods and refined to an R-factor of 19.3% against data to 2.0 A resolution. The protein comprises five short alpha-helices. Two of these form a helix-turn-helix motif, very similar to those found in related proteins. The protein is remarkably similar to the Cro protein from the same phage.

The yeast RAD50 gene encodes a predicted 153-kD protein containing a purine nucleotide-binding domain and two large heptad-repeat regions.

The RAD50 gene of Saccharomyces cerevisiae is required for chromosome synapsis and recombination during meiosis and for repair of DNA damage during vegetative growth. The precise role of the RAD50 gene product in these processes is not known. Most rad50 mutant phenotypes can be explained by the proposal that the RAD50 gene product is involved in the search for homology between interacting DNA molecules or chromosomes, but there is no direct evidence for this model. We present here the nucleotide sequence of the RAD50 locus and an analysis of the predicted 153-kD RAD50 protein. The amino terminal region of the predicted protein contains residues suggestive of a purine nucleotide binding domain, most likely for adenine. The remaining 1170 amino acids consist of two 250 amino acid segments of heptad repeat sequence separated by 320 amino acids, plus a short hydrophobic carboxy-terminal tail. Heptad repeats occur in proteins such as myosin and intermediate filaments that form alpha-helical coiled coils. One of the two heptad regions in RAD50 shows similarity to the S-2 domain of rabbit myosin beyond that expected for two random coiled coil proteins.

Uterine Sarcoma: The Indian Scenario.

Uterine sarcomas are rare, highly malignant tumours comprising < 1 % of all gynaecologic malignancies. To evaluate clinical presentation, histolopathologic pattern and outcome of uterine sarcomas presenting to a tertiary referral centre over an 8 year period (2004-2012). All histologically proven uterine sarcomas were retrospectively analysed. Clinical presentation, histology, treatment and outcome were analysed. Mean age was 42 years. Predominant histopathology was endometrial stromal sarcoma (n = 13); 9 were low grade, carcinosarcoma (n = 8) and leiomyosarcoma (n = 2). Fourteen patients had Stage I disease, 3 Stage II, 4 Stage III and 2 were Stage IV at presentation. Patients with disease confined to uterus received no adjuvant treatment (61 %). Of these, 11 were endometrial stromal sarcoma (7 were low grade) and 3 were carcinosarcomas. Four patients received adjuvant EBRT following hysterectomy (17 %). Two patients who presented with metastases received palliative chemotherapy. Mean follow-up period was 46 months (0-86 months). Eleven patients (47 %) developed disease recurrence. Seven (30 %) had local recurrence, while 4 (17 %) developed pulmonary metastases. A total of eight patients died and all deaths were within 1 year of recurrence. The only prognostic factor that correlated with survival was the stage of disease at diagnosis.

The use of side-chain packing methods in modeling bacteriophage repressor and cro proteins.

In recent years, it has been repeatedly demonstrated that the coordinates of the main-chain atoms alone are sufficient to determine the side-chain conformations of buried residues of compact proteins. Given a perfect backbone, the side-chain packing method can predict the side-chain conformations to an accuracy as high as 1.2 A RMS deviation (RMSD) with greater than 80% of the chi angles correct. However, similarly rigorous studies have not been conducted to determine how well these apply, if at all, to the more important problem of homology modeling per se. Specifically, if the available backbone is imperfect, as expected for practical application of homology modeling, can packing constraints alone achieve sufficiently accurate predictions to be useful? Here, by systematically applying such methods to the pairwise modeling of two repressor and two cro proteins from the closely related bacteriophages 434 and P22, we find that when the backbone RMSD is 0.8 A, the prediction on buried side chain is accurate with an RMS error of 1.8 A and approximately 70% of the chi angles correctly predicted. When the backbone RMSD is larger, in the range of 1.6-1.8 A, the prediction quality is still significantly better than random, with RMS error at 2.2 A on the buried side chains and 60% accuracy on chi angles. Together these results suggest the following rules-of-thumb for homology modeling of buried side chains. When the sequence identity between the modeled sequence and the template sequence is > 50% (or, equivalently, the expected backbone RMSD is < 1 A), side-chain packing methods work well. When sequence identity is between 30-50%, reflecting a backbone RMS error of 1-2 A, it is still valid to use side-chain packing methods to predict the buried residues, albeit with care. When sequence identity is below 30% (or backbone RMS error greater than 2 A), the backbone constraint alone is unlikely to produce useful models. Other methods, such as those involving the use of database fragments to reconstruct a template backbone, may be necessary as a complementary guide for modeling.

Different protein sequences can give rise to highly similar folds through different stabilizing interactions.

We report an interesting case of structural similarity between 2 small, nonhomologous proteins, the third domain of ovomucoid (ovomucoid) and the C-terminal fragment of ribosomal L7/L12 protein (CTF). The region of similarity consists of a 3-stranded beta-sheet and an alpha-helix. This region is highly similar; the corresponding elements of secondary structure share a common topology, and the RMS difference for "equivalent" C alpha atoms is 1.6 A. Surprisingly, this common structure arises from completely different sequences. For the common core, the sequence identity is less than 3%, and there is neither significant sequence similarity nor similarity in the position or orientation of conserved hydrophobic residues. This superposition raises the question of how 2 entirely different sequences can produce an identical structure. Analyzing this common region in ovomucoid revealed that it is stabilized by disulfide bonds. In contrast, the corresponding structure in CTF is stabilized in the alpha-helix by a composition of residues with high helix-forming propensities. This result suggests that different sequences and different stabilizing interactions can produce an identical structure.

APBioNet: the Asia-Pacific regional consortium for bioinformatics.

Bioinformatics and computational biology, along with the related fields of genomics, proteomics, functional genomics and systems biology are new wave scientific disciplines that harness composite computational power across networks to advance biological knowledge at the most basic level and to direct traditional laboratory-based research efforts in the biomedical sciences. 'Fostering the growth of bioinformatics and allied disciplines in the Asia-Pacific region' is the motto of the first regional bioinformatics society, the Asia-Pacific Bioinformatics Network (APBioNet). APBioNet addresses the issues of hardware, software, databases and networks pertaining to bioinformatics, with the additional layer of pertinent education, training and research. Recent milestones achieved include hosting an international bioinformatics symposium in Asia and setting up large-scale regional grid-computing projects.