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Introduction
Khairul Bariyyah Abd Halim currently works at the Department of Biotechnology, International Islamic University Malaysia. Khairul Bariyyah does research in Biomolecular modeling and simulation using GROMACS. Their most recent publication is 'Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure'.
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Publications
Publications (22)
Over the years, the escalation of cancer cases has been linked to the resistance, less selectivity, and toxicity of available anticancer drugs to normal cells. Therefore, continuous efforts are necessary to find new anticancer drugs with high selectivity of epidermal growth factor receptor tyrosine kinase (EGFR-TK) as a therapeutic target. The EGFR...
BRCA1-associated protein 1 (BAP1) is a nuclear-localized Ubiquitin C-terminal hydrolase (UCH) that functions as a tumour suppressor, and although BAP1 has been linked to cancer, the molecular mechanism by which BAP1 regulates cancer and its crystal structure have not been elucidated. In this study, computational approaches were used to identify the...
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common enzyme deficiency disorder affecting
over 400 million individuals worldwide. G6PD protects red blood cells (RBC) from the harmful effects of oxidative
substances. There are more than 400 G6PD mutations, of which 186 variants have shown to be linked to G6PD deficiency
by decreasi...
Introduction: Phyllanthus niruri has a high antioxidant capacity due to high phenolic and flavonoid content. This study is to determine and evaluate the effect of particle size, methods and time of extraction on its antioxidant activities. Methods: P. niruri was dried overnight in drier at 40˚C and grounded to different particle sizes. The extracti...
Literature have shown that oil palm leaves (OPL) can be transformed into nanocellulose (NC) by fungal lignocellulosic enzymes, particularly those produced by the Trichoderma species. However, mechanism of β-glucosidase and xylanase selectivity to degrade lignin, hemicellulose and cellulose in OPL for NC production remains relatively vague. The stud...
We previously reported on a mutant lipase KV1 (Mut-LipKV1) from Acinetobacter haemolyticus which optimal pH was raised from 8.0 to 11.0 after triple substitutions of surface aspartic acid (Asp) with lysine (Lys). Herein, this study further examined the Mut-LipKV1 by molecular docking, molecular dynamics (MD) simulations and molecular mechanics-Pois...
Alkaline-stable lipases are highly valuable biocatalysts that catalyze reactions under highly basic conditions. Herein, computational predictions of lipase from Acinetobacter haemolyticus and its mutant, Mut-LipKV1 was performed to identify functionally relevant mutations that enhance pH performance under increasing basicity. Mut-LipKV1 was constru...
Fungi of the Trichoderma species are valued industrial enzymes in support of the ‘zero-waste’ technology to convert agro-industrial biomass into valuable products, i.e. nanocellulose (NC). In this study, an in silico approach using substrate docking and molecular dynamic simulation was used to predict the order of which the multilayers of cellulosi...
Dehalogenase E (DehE) is a non-stereospecific enzyme produced by the soil bacterium, Rhizobium sp. RC1. Till now, the catalytic mechanism of DehE remains unclear although several literature concerning its structure and function are available. Since DehE is non-stereospecific, the enzyme was hypothesized to follow a ‘direct attack mechanism’ for the...
Recent outbreaks of highly pathogenic influenza strains have highlighted the need to develop new anti-influenza drugs. Here, we report an in silico study of carvone derivatives to analyze their binding modes with neuraminidase (NA) active sites. Two proposed carvone analogues, CV(A) and CV(B), with 36 designed ligands were predicted to inhibit NA (...
Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles...
Membrane-bound fatty acid desaturases perform oxygenated desaturation reactions to insert double bonds within fatty acyl chains in regioselective and stereoselective manners. The 9-fatty acid desaturase strictly creates the first double bond between C9 and 10 positions of most saturated substrates. As the three-dimensional structures of the bacteri...
Model and docking structures
Model Quality verification
Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling s...
Synthetic haloalkanoic acid (HA) is one of the synthetics compounds that can be found as active ingredients in
herbicides. These compounds are known to pollute our agriculture land due to their toxicity, thus may cause serious environmental and health problems. Biological process such as microbial dehalogenation degrades the harmful compounds and p...
Background:
The epidermal growth factor receptor (EGFR) is the best characterised member of the receptor tyrosine kinases, which play an important role in signalling across mammalian cell membranes. The EGFR juxtamembrane (JM) domain is involved in the mechanism of activation of the receptor, interacting with the anionic lipid phosphatidylinositol...
The interactions of transmembrane (TM) α-helices with the phospholipid membrane and with one another are central to understanding the structure and stability of integral membrane proteins. These interactions may be analyzed via coarse grained molecular dynamics (CGMD) simulations. To obtain statistically meaningful analysis of TM helix interactions...
Signal transduction is essential for many biological processes, such as mitosis, cell regeneration and differentiation. The transmembrane (TM) domains of many signalling proteins are known to play an essential part in these processes, focussing structural and biophysical studies on transmembrane helix dimers. This is especially true of the receptor...
Signal transduction is essential for many biological processes, such as mitosis, cell regeneration, and muscle contraction. Muscle-Specific Kinase (MuSK) is in a complex with low-density lipoprotein receptor-related protein 4 (LRP4), and upon binding of the substrate Agrin to LRP4, conformational changes of these proteins initiate a signalling casc...
