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Papers by rajendra Koirala

AIP Advances

Transportation of amino acids throughout the body is an essential mechanism to support life proce... more Transportation of amino acids throughout the body is an essential mechanism to support life processes. Transportation phenomena such as diffusion, viscosity, etc., of amino acids in an aqueous medium are useful to understand their inter- and intra-molecular interactions. In this work, we performed classical molecular dynamics simulation to study the transportation properties of γ-aminobutyric acid (GABA) in an aqueous environment. Self-diffusion coefficients of both GABA and water molecules as well as their binary diffusion coefficient were estimated at different temperatures. This work was further extended to estimate the effect of system size on diffusion coefficients and the viscosity coefficients of the solvent. In addition, the temperature dependence of the diffusion coefficient was studied utilizing an Arrhenius plot. The outcomes were compared with previously reported values. Furthermore, the number of hydrogen bonds between the solute and the solvent as well as the solvent a...

Journal of Biomolecular Structure and Dynamics

BIBECHANA

Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage a... more Methylation at O6 atom of guanine is a type of DNA damage which can cause a cancer. This damage at O6 atom of guanine in a DNA can be transferred to SG atom of cysteine in O6-alkylguanine-DNA alkyltransferase (AGT). Flipping out of methylated guanine from its base stack is essential to give off the methyl adduct (CH3) to AGT. AGT receives the methyl adduct at cysteine leaving guanine demethylated, but still in flipped out orientation. The repair mechanism of DNA would be completed only when the extrahelically flipped guanine returns back into the base stack, which is considered as the final step of the DNA repair mechanism. Here, the intrahelical flipping mechanism of repaired guanine has been studied. The work is further extended to examine the stability of hydrogen bonds between guanine and its pair partner cytosine. The overall result shows that intrahelical rotation of repaired guanine is possible and the base pairing is stable as the ordinary hydrogen bonding. BIBECHANA 19 (202...

Bulletin of the American Physical Society, Mar 15, 2021

BIBECHANA, 2018

The study of natural background radiation dose at thirty two locations of Kathmandu valley has be... more The study of natural background radiation dose at thirty two locations of Kathmandu valley has been done successfully using the instrument Radalert 100. The average dose rates and annual effective dose were measured. From the measurements, the least value of average dose rate was found to be (22.3±3.9)×10-3 mR/hr for Sundhara and the greatest value of average dose rate was found to be (37.7±7)×10-3 mR/hr for Budhanilkantha 3. As per the annual effective dose, the least value was 0.391 mSv/yr for Sundhara and the greatest value was 0.661 mSv/yr for Budhanilkantha 3. The average annual effective dose of Kathmandu valley was 0.475 mSv/yr ranging from 0.391 mSv/yr to 0.661 mSv/yr. The values thus obtained were compared to the worldwide average value of annual effective dose, 0.48 mSv/yr. Also, the obtained values were compared to the legal dose limit (annual effective dose), 1 mSv/yr set by International Commission on Radiological Protection (ICRP) for non-radiation workers and members of public. Among these thirty two locations, eight locations were chosen such that they had larger range of the observed dose rates. Those eight locations were re-observed. Further, Chi-square test was carried out to test whether the observed dose rates were following normal distribution or not. From the calculation, it was observed that the observed dose rates were following the normal distribution.

International Journal of Applied Sciences and Biotechnology, 2015

With the increase in the use of the mobile phone, widely used wireless technology, people are hig... more With the increase in the use of the mobile phone, widely used wireless technology, people are highly conscious regarding the deleterious effects of the RF signals. To account this consciousness, this research work deals with the assessment of the radiation level near mobile Base Station Towers (BSTs) of Kathmandu valley with the analysis of the observed values in reference to the National and International guidelines and radiation norms adopted in different countries. “Tenmars, TM-196” and GPS map60Csx were employed for the measurement. It is found that the maximum value of the Power density in Kathmandu valley is 0.003602 W/m2 at Maximum Peak Point (MPP) near BST of New Baneshwor area, characterized by high traffic (Vicinity population) and all services across the BSTs and the minimum average radiation level far away from the BSTs (Off tower region) with access of the cellular network has 0.00000206 W/m2 Power density near Lele area, Lalitpur, which is far less than the Power densi...

Journal of Institute of Science and Technology, 2020

Human thymocyte nuclear protein 1 (hTHYN1) is one of the DNA binding proteins. It is essential fo... more Human thymocyte nuclear protein 1 (hTHYN1) is one of the DNA binding proteins. It is essential for the regulation of Pax5 expression and the development of B cells in humans. Its thermodynamic and biological functions have been unclear yet. The study of the binding mechanism of hTHYN1 protein with DNA is essential to understand various biochemical functions in the human body. In this work, molecular dynamics (MD) simulations have been performed to understand the binding mechanisms of double methylated DNA (dmDNA) at cytosine nucleotide with hTHYN1 protein. Hydrogen bonding and other non-bonded (electrostatics and van der Waals) interactions among the residue-nucleotide pairs have been observed during the MD simulations and are also found responsible to form protein-DNA complex and to provide the stability of the structure. No salt bridges and hydrophobic interactions have been detected. Some of the protein residues in hTHYN1 have been found to strongly cooperate in the formation of ...

Himalayan Physics, 2019

Disulphide bond in cysteine residues plays vital role in structural stability and fuctional varia... more Disulphide bond in cysteine residues plays vital role in structural stability and fuctional variation of protein molecules. Study of cysteine dimer linking with disulphide bond reveals the nature of stability of tertiary and quarternary structure in polypeptide chain. In order to study the transport properties of cysteine dimer, the molecular dynamics (MD) simulations have been performed at different temperature. The self diffusion coefficients of both cysteine dimer and TIP3P water model have been estimated at four different temperature from the slope of mean square displacement (MSD) versus time plot using Einstein's relation and their binary diffusion coefficients from Darken's relation.

Journal of Nepal Physical Society, 2020

Human growth hormone (hGH) is synthesized, stored and secreted by somatotropic cells within the l... more Human growth hormone (hGH) is synthesized, stored and secreted by somatotropic cells within the lateral wings of the anterior lobe of pituitary glands; and is transported to other organs of human body. Study of intra-molecular structure and its binding mechanisms within the molecule gives more insight of structural stability of the molecule and is also essential in drug designing. In this article, we have investigated the various bonded and non-bonded interactions that contribute for the conformation of entire structure of the hGH molecule using molecular dynamics (MD) simulation. The MD outcomes show that the molecule is hydrophobic in nature. In its conformation, several types of interactions exist, such as disulphide bridges (bonded) and nonbonded: hydrogen bond, hydrophobic, aromatic-aromatic, ionic, aromatic-sulphur, cation-pi.

Journal of Nepal Physical Society, 2017

Ultrasonography (USG) is a major modality to determine the dimension of internal body parts and f... more Ultrasonography (USG) is a major modality to determine the dimension of internal body parts and foreign materials that enters into the tissue. This modality can measure the accurate value of the size of organs because it has no magnification property. This measurement based on the sound pulse to travel to the object and the echo to return back. In the present study, the ultrasonographic kidney length is determined in individuals without known renal disease. The experiment is done 504 patients (214 males and 290 females) who came to Tribhuvan University Teaching Hospital (TUTH) from May 2001 to August 2001. The average kidney size of Nepalese people was found (9.48 0.96) cm. The kidney length was found maximum in the age range around 40 years and observed approximately not changing significantly up to the age of 60 and decreasing from the age range 60 years. Moreover, average kidney size of male is found to be greater than the female of same age group.

The study of structural conformation of Gamma-aminobutyric acid (GABA) exhibits its biological an... more The study of structural conformation of Gamma-aminobutyric acid (GABA) exhibits its biological and chemical activities. The GABA molecule is responsible in neurotransmission from one neuron to another neuron and activates the ion channels to pass the chlorine and sodium ions in nerve cells. Its conformation in solid state and gas state are extremely different and it also shows five different conformations in aqueous solution. The study of its structure in such environment can reveal its activity in cellular environment. We have performed the classical molecular dynamics study of this system of GABA in aqueous medium to deal its structure. Radial distribution function (RDF) has been used to study the structural properties of the system. BIBECHANA 18 (2021) 67-74

Classical molecular dynamics simulation is performed to estimate the diffusion coefficient of oxy... more Classical molecular dynamics simulation is performed to estimate the diffusion coefficient of oxytocin in water at different temperatures, 288 K, 300 K, 313 K, 323 K, using GROningen Machine for Chemical Simulations (GROMOCS). The simulation is carried out using GROMOS43A1 force field and extended simple point charge (SPC/E) water model. The stability of the system is evaluated from energy profile of potential and kinetic energy, which assures well equilibrated molecular system. The self-diffusion coefficient of oxytocin and water is obtained from Einstein’s relation and binary diffusion coefficient is obtained from Darken’s relation. As temperature increases the diffusion coefficient also increases as per expectation. The diffusion coefficients of water from the present calculations agree well with the previously reported values, within the 10% of deviation. Furthermore, the activation energy has been studied using Arrhenius Plot. BIBECHANA 18 (2021) 108-117

Journal of Molecular Liquids

Biological Chemistry

Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine... more Methylation induced DNA base-pairing damage is one of the major causes of cancer. O6-alkylguanine-DNA alkyltransferase (AGT) is considered a demethylation agent of the methylated DNA. Structural investigations with thermodynamic properties of the AGT-DNA complex are still lacking. In this report, we modeled two catalytic states of AGT-DNA interactions and an AGT-DNA covalent complex and explored structural features using molecular dynamics (MD) simulations. We utilized the umbrella sampling method to investigate the changes in the free energy of the interactions in two different AGT-DNA catalytic states, one with methylated GUA in DNA and the other with methylated CYS145 in AGT. These non-covalent complexes represent the pre- and post-repair complexes. Therefore, our study encompasses the process of recognition, complex formation, and separation of the AGT and the damaged (methylated) DNA base. We believe that the use of parameters for the amino acid and nucleotide modifications and...

SARS-CoV-2 virus interacts via C-terminal domain of spike protein to human cell receptor protein ... more SARS-CoV-2 virus interacts via C-terminal domain of spike protein to human cell receptor protein hACE2. Amino acid residues residing at the interface play vital role in binding of SARS-CoV-2 CTD to hACE2. The detailed atomic level inves- tigation of interactions at binding interface of SARS-CoV-2 CTD/hACE2 provides indispensable information on better understanding of location for drug target. In the present work, we have studied the dynamical behaviour of the complex by ana- lyzing the molecular dynamics (MD) trajectories. The major interacting residues of SARS-CoV-2 CTD and hACE2 have been identiﬁed by analyzing the non-bonded interactions such as hydrogen bondings, salt bridges, hydrophobic interactions, van der Waals interactions etc. Umbrella sampling method has been used to estimate the binding free energy for in-depth understanding of binding mechanism between virus protein and host receptor. The binding free energy diﬀerence, key residues at the interface, important atomic in...

Journal of Physics Communications