Smoothing of the GB1 Hairpin Folding Landscape by Interfacial Confinement

We study the effects of confinement between planar walls on the folding thermodynamics of a β-hairpin, using large-scale replica-exchange molecular-dynamics simulations with an all-atom model and explicit solvent. We find that the folding free-energy landscape of this peptide observed in bulk is significantly modified when the peptide is confined between the walls. Most notably, the propensity of the peptide to form a misfolded state observed in the bulk solution becomes negligible under confinement. The absence of the misfolded state under confinement can be explained by an increased tendency of hydrophobic aromatic side chains to stay near the walls, because the misfolded state is characterized by a nonnative arrangement of aromatic side chains. These results from a simple confinement model may provide clues about the role of chaperonin confinement in smoothing folding landscapes by avoiding trapped intermediates.     

Structure based virtual screening of ligands to identify cysteinyl leukotriene receptor 1 antagonist

Montelukast and Zafirlukast are known leukotriene receptor antagonists prescribed in asthma treatment. However, these fall short as mono therapy and are frequently used in combination with inhaled glucocorticosteroids with or without long acting beta 2 agonists. Therefore, it is of interest to apply ligand and structure based virtual screening strategies to identify compounds akin to lead compounds Montelukast and Zafirlukast. Hence, compounds with structures having 95% similarity to these compounds were retrieved from NCBI׳s PubChem database. Compounds similar to lead were grouped and docked at the antagonist binding site of cysteinyl leukotriene receptor 1. This exercise identified compounds UNII 70RV86E50Q (Pub Cid 71587778) and Sure CN 9587085 (Pub Cid 19793614) with higher predicted binding compared to Montelukast and Zafirlukast. It is shown that the compound Sure CN 9587085 showed appreciable ligand receptor interaction compared to UNII 70RV86E50Q. Thus, the compound Sure CN 9587085 is selected as a potent antagonist to cysteinyl leukotriene receptor 1 for further consideration in vitro and in vivo validation.     

What limits the primary sequence space of natural proteins?

Abstract

Number of naturally occurring primary sequences of proteins is an infinitesimally small subset of the possible number of primary sequences that can be synthesized using 20 amino acids. Prevailing views ascribe this to slow and incremental mutational/selection evolutionary mechanisms. However, considering the large number of avenues available in form of diversity of emerging/evolving and/or disappearing living systems for exploring the primary sequence space over the evolutionary time scale of ～3.5 billion years, this remains a conjecture. Therefore, to investigate primary sequence space limitations, we carried out a systematic study for finding primary sequences absent in nature. We report the discovery of the smallest peptide sequence “Cysteine-Glutamine-Tryptophan-Tryptophan” that is not found in over half-a-million curated protein sequences in the Uniprot (Swiss-Prot) database. Additionally, we report a library of 83605 pentapeptides that are not found in any of the known protein sequences. Compositional analyses of these absent primary sequences yield a remarkably strong power relationship between the percentage occurrence of individual amino acids in all known protein sequences and their respective frequency of occurrence in the absent peptides, regardless of their specific position in the sequences. If random evolutionary mechanisms were responsible for limitations to the primary sequence space, then one would not expect any relationship between compositions of available and absent primary sequences. Thus, we conclusively show that stoichiometric constraints on amino acids limit the primary sequence space of proteins in nature. We discuss the possibly profound implications of our findings in both evolutionary and synthetic biology.

Communicated by Ramaswamy H. Sarma     

Protein and carbohydrate histochemistry in relation to the keratinization in the epidermis of Barbus sophor (Cyprinidae, Pisces)

The distribution of protein and carbohydrate constituents in the epidermis of Barbus sophor is described in order to give a better understanding of its cellular organization and physiology.
Various cytochemical techniques show the keratinized nature of the outer free margins of the polygonal cells in the most-superficial layer. These contain appreciable amounts of cysteine bound sulphydryl groups, basic proteins, protein bound NH₂ groups, ribonucleic acid and calcium and give a strong Papanicolaou's reaction. Absence of cystine bound disulphide groups suggests that the cornified layer in B. sophor is probably mechanically weak as adjacent keratin chains remain unbonded. The polygonal cells showing keratinization at the outer free margins remain metabolically active and are not sloughed off at the surface. This is in contrast to the keratinized epidermis of other teleosts so far reported in which the keratinized cells are dead and are sloughed off at the surface.
In addition to keratinization the polygonal cells undergo mucogenesis synthesizing sulphated acid mucopolysaccharides.
The presence of eosinophilic granular cells in the epidermis is interesting. The possible role of these cells in the protection of the epidermis has been discussed. The epidermis on the inner surface of the scale is very thin so it may not have much protective significance in these areas.     

The merrit alloantigenic system of human B lymphocytes: evidence for thirteen possible factors including one six-member segregant series.

An analysis of the typing results of a 70-member chronic lymphatic leukemia B cell panel revealed evidence for 13 possible groups of the Merrit alloantigenic system. Six of these appeared possibly allelic and may represent a segregant series. The CLL panel was also fully typed for HLA and some degree of linkage dysequilibrium between Merrit and HLA seemed apparent from the data. Merrit antibodies can be absorbed out with selected surface membrane immunoglobulin (SMIG)-positive normal lymphocytes and less so or not at all with E rosette-forming T cells or Fc-positive SMIG-negative lymphocytes.     

Excipient Stability in Oral Solid Dosage Forms: A Review

The choice of excipients constitutes a major part of preformulation and formulation studies during the preparation of pharmaceutical dosage forms. The physical, mechanical, and chemical properties of excipients affect various formulation parameters, such as disintegration, dissolution, and shelf life, and significantly influence the final product. Therefore, several studies have been performed to evaluate the effect of drug-excipient interactions on the overall formulation. This article reviews the information available on the physical and chemical instabilities of excipients and their incompatibilities with the active pharmaceutical ingredient in solid oral dosage forms, during various drug-manufacturing processes. The impact of these interactions on the drug formulation process has been discussed in detail. Examples of various excipients used in solid oral dosage forms have been included to elaborate on different drug-excipient interactions.     

Association of <Emphasis Type="Italic">Toll like receptor 2</Emphasis> and <Emphasis Type="Italic">9</Emphasis> gene variants with pulmonary tuberculosis: exploration in a northern Indian population

Tuberculosis (TB) is a disease of global importance. There is an increasing recognition of the role of Toll like receptors, important pattern recognition receptors of host immune system, in determining the susceptibility or resistance to TB in various populations. In an attempt to examine the importance of Toll like receptors in immune response to Mycobacterium tuberculosis infection, we explored two variants each of TLR2 and TLR9 in a population residing in Uttar Pradesh, India. Genotyping was performed to detect -196 to -174 del polymorphism and G2258A SNP (Arg753Gln, rs5743708) in TLR2 gene and -T1237C (rs5743836) and G2848A (rs352140) SNP in TLR9 gene in patients with pulmonary TB and healthy controls. The A allele of G2848A SNP in TLR9 gene was found with a marginally higher frequency among TB patients as compared to healthy controls, suggesting that A allele at position 2848 of TLR9 gene may be associated with susceptibility to TB in North Indian population [p?=?0.05, Mantel–Haenszel OR?=?1.34, 95% CI (1.0–1.82)].     

Mononuclear cell-modulation of granulosa cell steroidogenesis in rat: influence of ovarian cycle.

The mononuclear cells exert a paracrine influence on the ovarian function, including steroidogenesis. This study examines the ability of the conditioned medium from the cultures of splenic mononuclear cells, obtained during various phases of the ovarian cycle, on progesterone accumulation by the granulosa cells in the culture medium. Female Wistar rats, aged twenty-five days, were made pseudopregnant by an injection of pregnant mare's serum gonadotropin. The splenic mononuclear cells were isolated at follicular phase, early luteal phase, mid luteal phase and late luteal phase and cultured for 48 h. The ammonium sulphate precipitated fraction of the conditioned medium was added to the granulosa cells obtained from immature rats treated with diethylstillboestrol. The granulosa cells were cultured for 48 h, and the progesterone accumulated in the medium was assayed. The conditioned medium from the cultures of the mononuclear cells obtained during follicular phase and late luteal phase inhibited FSH-induced progesterone secretion, whereas conditioned medium obtained from mid luteal phase mononuclear cells enhanced the effect of FSH. The stimulatory effect of db-cAMP on progesterone accumulation in the culture medium is inhibited by conditioned medium obtained from all the phases of the ovarian cycle. This study demonstrates a cyclicity in the behaviour of the splenic mononuclear cells on ovarian steroidogenesis, suggesting a bi-directional paracrine and/or endocrine relationship between ovary and the mononuclear cells.     

Effect of 50 Hz sinusoidal electromagnetic field on the kinetics of 14CO2 exhalation after [14C]‐N‐Nitrosodiethylamine administration in mice

N‐Nitrosodiethylamine (NDEA) has been identified as a typical environmental carcinogen. Its metabolism was studied in mice under the influence of an electromagnetic field (EMF). After intraperitoneal administration of [¹⁴C]‐NDEA, 0.2 μCi/100 g body weight resulted in 22.8% of the total radioactivity exhaled as ¹⁴CO₂ within 1 h. Mice were exposed to a 50 Hz, 2 mT (rms) electromagnetic field, 8 h/day for 8 weeks. There was a significant increase in the metabolic turnover of [¹⁴C]‐NDEA into ¹⁴CO₂ at the end of both 6 and 8 weeks of field exposure, i.e., 26.9% and 37.4% respectively. The enhanced capacity of mice to metabolize NDEA after the exposure to EMF may result in animals with a smaller amount of the bioactive carcinogen burden, thereby indicating a protective role of 2 mT EMF in a whole animal study. Bioelectromagnetics 20:1–4, 1999. © 1999 Wiley‐Liss, Inc.