Accurately Modeling RNA Stem-Loops in an Implicit Solvent Environment.

Ribonucleic acid (RNA) molecules can adopt a variety of secondary and tertiary structures in solution, with stem-loops being one of the more common motifs. Here, we present a systematic analysis of 15 RNA stem-loop sequences simulated with molecular dynamics simulations in an implicit solvent environment. Analysis of RNA cluster ensembles showed that the stem-loop structures can generally adopt the A-form RNA in the stem region. Loop structures are more sensitive, and experimental structures could only be reproduced with modification of CH···O interactions in the force field, combined with an implicit solvent nonpolar correction to better model base stacking interactions. Accurately modeling RNA with current atomistic physics-based models remains challenging, but the RNA systems studied herein may provide a useful benchmark set for testing other RNA modeling methods in the future.

Computational investigations of B12-dependent enzymatic reactions.

Nature employs two biologically active forms of vitamin B12, adenosylcobalamin (or coenzyme B12) and methylcobalamin, as cofactors in molecular transformations both in bacteria and mammals. Computational chemistry, guided by experimental data, has been used to explore fundamental characteristics of these enzymatic reactions. In particular, the quantum mechanics/molecular mechanics (QM/MM) method has proven to be a powerful tool in elucidating important characteristics of B12-dependent enzymatic reactions. Herein, we will present a brief tutorial in conducting QM/MM calculations for B12 enzymatic reactions. We will summarize recent contributions that target the use of QM/MM calculations in both photochemical and enzymatic reactions including AdoCbl-dependent ethanolamine ammonia lyase, glutamate mutase, and photoreceptor CarH.

Clinicopathological and Immunological Profile of Patients with Cutaneous Manifestations and their Relationship with Organ Involvement in Systemic Lupus Erythematosus Attending a Tertiary Care Center of Eastern India.

BACKGROUND: Lupus erythematosus (LE) is an autoimmune disorder with diverse clinical manifestations ranging from mild cutaneous disorder to life-threatening systemic illness and associated with varying immunological parameters. AIM: We conducted a study in a tertiary care center of eastern India to determine the clinical pattern, immunological profile of patients with cutaneous manifestations of systemic LE (SLE) and their relationship with organ involvement. MATERIALS AND METHODS: Fifty-five consecutive patients attending dermatology OPD having features consistent with cutaneous LE and fulfilling the criteria of SLE were included. After proper history taking and clinical examination, routine blood and antinuclear antibody (ANA) profile, histopathological examination, and direct immunofluorescence test were undertaken. RESULTS: Among 55 patients, 49 were female. ANA positivity was the most common association, followed by photosensitivity, malar rash, arthritis, oral ulcer, immunological markers, renal system involvement, discoid rash, serositis, central nervous system (CNS) involvement, and least common being the hematological involvement. Vacuolar basal cell degeneration was the commonest epidermal change and upper dermal periappendageal and perivascular lymphocytic infiltration was the commonest dermal change observed on histopathological examination. On direct immunofluorescence (DIF) granular pattern was seen in majority of patients. Statistically significant risk of kidney involvement was present both when patient had bullous lesions and DIF positivity of unexposed (DIF-UE) skin. CNS involvement was seen in five patients and it was found to be significantly associated with purpuric lesions. CONCLUSION: This study reveals cutaneous lesions and DIF testing could be reliable predictors of systemic involvement and strongly suggests DIF testing, routinely in all patients of SLE.