Differential dynamics of the serotonin1A receptor in membrane bilayers of varying cholesterol content revealed by all atom molecular dynamics simulation.

The serotonin1A receptor belongs to the superfamily of G protein-coupled receptors (GPCRs) and is a potential drug target in neuropsychiatric disorders. The receptor has been shown to require membrane cholesterol for its organization, dynamics and function. Although recent work suggests a close interaction of cholesterol with the receptor, the structural integrity of the serotonin1A receptor in the presence of cholesterol has not been explored. In this work, we have carried out all atom molecular dynamics simulations, totaling to 3 µs, to analyze the effect of cholesterol on the structure and dynamics of the serotonin1A receptor. Our results show that the presence of physiologically relevant concentration of membrane cholesterol alters conformational dynamics of the serotonin1A receptor and, on an average lowers conformational fluctuations. Our results show that, in general, transmembrane helix VII is most affected by the absence of membrane cholesterol. These results are in overall agreement with experimental data showing enhancement of GPCR stability in the presence of membrane cholesterol. Our results constitute a molecular level understanding of GPCR-cholesterol interaction, and represent an important step in our overall understanding of GPCR function in health and disease.

Potential of mean force calculations of ligand binding to ion channels from Jarzynski's equality and umbrella sampling.

Potential of mean force (PMF) calculations provide a reliable method for determination of the absolute binding free energies for protein-ligand systems. The common method used for this purpose -- umbrella sampling with weighted histogram analysis -- is computationally very laborious, which limits its applications. Recently, a much simpler alternative for PMF calculations has become available, namely, using Jarzynski's equality in steered molecular dynamics simulations. So far, there have been a few comparisons of the two methods and mostly in simple systems that do not reflect the complexities of protein-ligand systems. Here, we use both methods to calculate the PMF for ion permeation and ligand binding to ion channels. Comparison of results indicate that Jarzynski's method suffers from relaxation problems in complex systems and would require much longer simulation times to yield reliable PMFs for protein-ligand systems.

Binding of organic cations to gramicidin A channel studied with AutoDock and molecular dynamics simulations.

The accurate description of protein-ligand binding energies and configurations is an important problem in molecular biology with many applications in medicine and pharmacology. Molecular dynamics (MD) simulations provide the required accuracy but they are too slow for searching binding positions. Conversely, docking methods are much faster but have limited accuracy. An appropriate combination of the two methods could avoid the shortcomings associated with each, thus offering a better approach to the protein-ligand binding problem. Here we investigate the feasibility of such a combined docking-MD approach in a well-defined system: binding of organic cations to the gramicidin A channel. We use the AutoDock program to generate a set of protein-ligand binding configurations, which are then refined in MD simulations. For each system, we examine the binding configuration in detail and calculate the binding free energy by constructing the potential of mean force for the ligand. Our results show that AutoDock provides suitable initial configurations, which can be used profitably in MD simulations to obtain an accurate description of protein-ligand binding with a reasonable computational effort.

Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields.

Molecular dynamics simulations of membrane proteins have become a popular tool for studying their dynamic features, which are not easily accessible by experiments. Whether the force fields developed for globular proteins are adequate this purpose is an important question that is often glossed over. Here we determine the permeation properties of potassium ions in the gramicidin A channel in a lipid bilayer from free energy simulations, and compare the results to experimental data. In particular, we check the dependence of the free energy barriers ions face at the channel center on the membrane size. The results indicate that there is a serious problem with the current rigid force fields independent of the membrane size, and new, possibly polarizable, force fields need to be developed to resolve this problem.

Role of protein flexibility in ion permeation: a case study in gramicidin A.

Proteins have a flexible structure, and their atoms exhibit considerable fluctuations under normal operating conditions. However, apart from some enzyme reactions involving ligand binding, our understanding of the role of flexibility in protein function remains mostly incomplete. Here we investigate this question in the realm of membrane proteins that form ion channels. Specifically, we consider ion permeation in the gramicidin A channel, and study how the energetics of ion conduction changes as the channel structure is progressively changed from completely flexible to a fixed one. For each channel structure, the potential of mean force for a permeating potassium ion is determined from molecular dynamics (MD) simulations. Using the same molecular dynamics data for completely flexible gramicidin A, we also calculate the average densities and fluctuations of the peptide atoms and investigate the correlations between these fluctuations and the motion of a permeating ion. Our results show conclusively that peptide flexibility plays an important role in ion permeation in the gramicidin A channel, thus providing another reason--besides the well-known problem with the description of single file pore water--why this channel cannot be modeled using continuum electrostatics with a fixed structure. The new method developed here for studying the role of protein flexibility on its function clarifies the contributions of the fluctuations to energy and entropy, and places limits on the level of detail required in a coarse-grained model.

Amino acid disorders in mental retardation: a two-decade study from Andhra Pradesh.

A screening program was carried out for amino acid disorders in children with mental handicaps from the state of Andhra Pradesh (India) during the last two decades. Forty-one (0.9%) cases were detected with amino acid disorders among 4500 children surveyed. We reported amino acid disorders of rare occurrence such as dicarboxylic aminoaciduria, hydroxykynureninuria, persistent hypertyrosinemia, hydroxyprolinemia, hypervalinemia, etc. A new metabolic defect threoninemia was also detected. We have observed a preponderance of males with amino acid disorders. Parental consanguinity was present in 54% of cases with amino acid disorders.

Evaluation of FSH, LH and testosterone levels in different subgroups of infertile males.

Gonadotropins (FSH, LH) and testosterone are the prime regulators of germ cell development. Abnormal spermatogenesis is often associated with altered serum gonadotropins and testosterone. FSH, LH and testosterone levels were estimated in 96 infertile men of whom 35 were azoospermic, 35 were oligozoospermic, 11 were with varicocele and 15 were with histopathological abnormalities like hypospermatogenesis, spermatid arrest and sertoli-cell only syndrome. Results showed statistically significant (p<0.05), increase in the mean FSH and LH levels in all the infertile males studied when compared with the fertile controls (n=35). However, there is no significant difference in the mean levels of testosterone between the infertile and fertile men.

Detection of L1 CAM mutation in a male child with mental retardation.

Recent studies have presented evidence for the involvement of L1CAM gene mutations in various X-linked mental retardation syndromes. The neural cell adhesion molecule, L1CAM is a transmembrane protein belonging to the super family of the immunoglobulins that play a key role in embryonic development of the nervous system and is involved in memory and learning. No studies were carried out from India on L1 CAM gene in X-linked mental retardation syndromes. Hence, an investigation was taken up to delineate the role of L1CAM gene in mental retardation.Two families (Family I and Family II) having only two members affected with mental retardation in each family were studied for mutations in L1CAM gene. In family II, the younger sibling showed deletion involving region between the nucleotide 13,773 (intron 25) and 14,158 (intron 27) region. The mutation what we observed in younger sibling of the family II is a novel mutation which was not hitherto reported in the world literature.

Y chromosome microdeletions in infertile males from Andhra Pradesh, South India.

Studies on the frequency of Y chromosome microdeletions were carried out in 70 idiopathic infertile males with normal karyotypes. Genomic DNA was isolated from blood and PCR analysis was carried out with AZFa, AZFb, and AZFc STS markers SY 84, SY 87, SY 127, SY 254, and SY 158 to detect the deletions. In 9/70 (12.8%) subjects AZF deletions were observed. In 4/9 (44.4%) subjects were azoospermic, 4/9 (44.4%) of cases were severe oligozoospermic, and 1/9 (11.1%) cases was oligozoospermic.

Cytogenetic effects in workers occupationally exposed to tobacco dust.

Tobacco dust mainly contains nitrosamines, which are readily absorbed by the body tissues like skin, respiratory epithelium, and mucous membrane of mouth, nose and intestines. Exposure to tobacco dust is known to affect the respiratory tracts in humans. In the present study, cytogenetic effects of exposure to tobacco dust are evaluated in 154 male tobacco factory workers and 138 age and sex matched controls by analysing chromosomal aberrations in their peripheral blood lymphocytes. The workers were in the age group of 20-55 years and were employed in the tobacco processing factory for 1-32 years. Heparinised blood samples were collected from workers and control subjects and lymphocyte cultures were carried out by using standard technique. Slides were prepared and 150 metaphases were screened for each sample for various structural and numerical types of abnormalities. A statistically significant increase was observed in the frequencies of chromosomal aberrations in non-smoking and smoking exposed groups when compared to the respective controls. An increase in the frequencies of chromosomal aberrations was also observed with increase in years of service in the exposed subjects.

Hyper prolinuria and hyper-hydroxy prolinuria in children with mental retardation.

Three thousand cases with mental retardation referred from different hospitals were screened for aminoacid disorders. Among them one case of hyperprolinuria and another case of hyperprolinuria with hyper hydroxyprolinuria were detected. These are the first cases to be reported from the state of Andhra Pradesh.

PCR analysis of Yq microdeletions in infertile males, a study from South India.

AIM: To estimate the frequency of microdeletions in the long arm of Y-chromosome of 20 infertile males from South India. METHODS: Polymerase chain reaction (PCR) amplification using Y-specific STS of azoospermia factor (AZF) regions i.e., SY 84 for AZFa, SY 127 for AZFb and SY 254 for AZFc. RESULTS: Of the 20 infertile subjects 3 (15 %), one azoospermic and two oligozoospermic, showed microdeletions in the AZF region of Y-chromosome. CONCLUSION: The frequency of deletions involving AZF region of the Y-chromosome is 15 % in azoospermic and severely oligozoospermic infertile men. PCR amplification of AZF locus is useful for the diagnosis of microdeletions in the Y-chromosome.

Cytogenetic studies of 1001 Down syndrome cases from Andhra Pradesh, India.

Cytogenetic data obtained from investigating 1001 patients of Down syndrome (DS) and their parents over a period of 20 years (January 1979-January 1999) are presented. The frequency of pure trisomy, mosaicism and translocation was 87.92, 7.69 and 4.39 per cent respectively. The origin of the extra chromosome 21 due to meiotic non-disjunction was 79.24 per cent maternal and 20.76 per cent paternal. A high frequency of acrocentric chromosome associations was also observed in mothers of children of Down syndrome, this might have predisposed to an enhanced risk for non-disjunction. Birth order of DS showed a higher number of first and second borns. Reproductive performances of the parents indicated a high rate of abortions, compared to controls. Cytogenetic investigations carried out over these years greatly helped in the management of these children and for counseling the affected families.

Dicarboxylic aminoaciduria associated with mental retardation.

Five hundred mentally retarded children (of both sexes and under 15 years of age) referred to our institute were screened for aminoacid disorders. One case of dicarboxylic aminoaciduria was found in a girl.