Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

Correction: Population pharmacokinetics of fludarabine in patients with aplastic anemia and Fanconi anemia undergoing allogeneic hematopoietic stem cell transplantation

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Injury to the oral mucosa by organophosphates without systemic toxicity: a rare case

We describe a case of multiple Zargar grade IIA ulcerations of the oral mucosa with no systemic toxicity in a patient after ingestion of an organophosphate. Serial debridement, control of superadded infections, and active physiotherapy were the mainstay of the treatment plan. We know of no other reported cases of poisoning by organophosphates that caused burns of the oral mucosa and no systemic toxicity.

Breast mass characterization using shear wave elastography and ultrasound

PURPOSE

To evaluate the role of SWE in characterizing breast masses and ascertain whether additional use of SWE to ultrasound for evaluating BI-RADS 3 and 4a masses could help reduce long-term follow-up and unnecessary biopsies of these suspicious breast masses.

MATERIALS AND METHODS

This prospective, cross-sectional study was performed between June 2013 and November 2014. All enrolled patients underwent clinical breast examination, ultrasound, SWE and ultrasound-guided core biopsy of the breast mass. Breast Imaging Reporting and Data System (BI-RAD) categories were assigned to breast masses. For qualitative and quantitative variables of SWE, cut-off values for differentiation between benign and malignant breast masses were estimated. Modified BIRADS' (up/downgrading of BIRADS category) was done for BI-RADS 3/4a masses by combining individual SWE parameters and ultrasound findings. Sensitivity, specificity, positive and negative predictive value of modified BI-RADS' and ultrasound BI-RADS were compared.

RESULTS

A total of 119 women (mean age, 42.3±13.6 [SD] years; range: 13-87 years) with a single breast mass each were enrolled. Histopathologically, 57/119 (48%) breast masses were benign and 62 (52%) were malignant. On ultrasound, 42 breast masses were BI-RADS3 and 77 were BI-RADS 4 (4a, n=10; 4b, n=24; 4c, n=43) leading to 96.8% sensitivity and 70.2% specificity. On SWE, benign breast masses were oval/round, homogenous/reasonably homogenous, blue/green with lower elasticity values and malignant breast masses were irregular, inhomogeneous, red/orange with high elasticity values. On modified BI-RADS' using E-color and E-mean/E-max, specificity improved to 78.9% and 75.4% respectively.

CONCLUSION

Addition of SWE to ultrasound improves characterization of BI-RADS 3 and 4a masses. E-max, E-mean and E-color are the most useful SWE parameters to differentiate between malignant and benign breast masses.

Type-3 von Willebrand disease in India-Clinical spectrum and molecular profile

INTRODUCTION

Type 3 von Willebrand disease (VWD) is the rare and most severe form of VWD which results from a near-complete deficiency of the von Willebrand factor (VWF). This study evaluates in detail the molecular pathology of type-3 VWD in India. One hundred and two patients from 90 families were evaluated.

PATIENTS AND METHODS

Phenotypic data, including bleeding scores (BS), were documented using structured questionnaires. Diagnosis of type 3 VWD was based on undetectable VWF antigen levels in the plasma. Genomic DNA from these patients was screened for mutations in VWF gene. Structural modeling and expression studies were carried out for missense mutations.

RESULTS

Out of 102 patients, mutations could be identified in 91% (n = 93). Fifty-five different gene variants were identified. Thirty-four (61.8%) were novel. Mutations could be identified in both the alleles in 90 patients, while no causative mutation could be identified in 9 patients; twenty-four (23.5%) patients had mutations clustered in the propeptide region of VWF. Interestingly, five mutations accounted for the defects in 37/93 (39.8%) patients. Structural analysis and in vitro studies on missense mutations imply impaired processes associated with secretion of VWF.

CONCLUSION

This study is one of the largest series to define the molecular basis of type-3 VWD.

Acute-onset Restless legs syndrome in acute neurological conditions-a prospective study on patients with the Guillain-Barre syndrome and acute stroke

OBJECTIVES

While the Restless legs syndrome (RLS) is usually recognized as a chronic condition, it has often been diagnosed among patients with acute neurological illnesses, in which limb discomfort is reported. This study was conducted to determine how many among these, actually have acute-onset RLS, and also to evaluate characteristics of this subgroup of patients with Guillain-Barre syndrome (GBS) and stroke developing acute-onset RLS.

METHODS

Consecutive patients diagnosed with GBS and eligible stroke patients, admitted to our Neurology services over a 1-year period, were enrolled. They were evaluated for symptoms of RLS based on IRLSSG consensus criteria and the AIIMS RLS Questionnaire for Indian patients (ARQIP).

RESULTS

Forty adults with GBS and 58 with stroke were included. A total of 10 of the 40 (25%) patients with GBS developed definite acute RLS, which was mostly monophasic. Seven (70%) of these had demyelinating type of GBS, a significant association with acute RLS (P = .024). Six of the 58 stroke patients (10%) developed definite acute-onset, often persistent RLS. Subcortical location showed significant association with increased risk of developing acute RLS (P < .001). All patients diagnosed with acute-onset RLS had an immediate and good response to dopamine agonists.

CONCLUSION

This is the first study showing that acute-onset RLS is common, affecting nearly 25% of patients with GBS and 10% patients with acute stroke. Recognizing and treating it can majorly contribute toward symptom relief and early improvement in the quality of life for this population.

Random distributions of initial porosity trigger regular necking patterns at high strain rates

At high strain rates, the fragmentation of expanding structures of ductile materials, in general, starts by the localization of plastic deformation in multiple necks. Two distinct mechanisms have been proposed to explain multiple necking and fragmentation process in ductile materials. One view is that the necking pattern is related to the distribution of material properties and defects. The second view is that it is due to the activation of specific instability modes of the structure. Following this, we investigate the emergence of necking patterns in porous ductile bars subjected to dynamic stretching at strain rates varying from 10³ s^-1 to 0.5×10⁵ s^-1 using finite-element calculations and linear stability analysis. In the calculations, the initial porosity (representative of the material defects) varies randomly along the bar. The computations revealed that, while the random distribution of initial porosity triggers the necking pattern, it barely affects the average neck spacing, especially, at higher strain rates. The average neck spacings obtained from the calculations are in close agreement with the predictions of the linear stability analysis. Our results also reveal that the necking pattern does not begin when the Considère condition is reached but is significantly delayed due to the stabilizing effect of inertia.