Mohd Firdaus Raih

National University of Malaysia | ukm · School of Biological Sciences and Biotechnology

We earlier showed that Torpedo californica acetylcholinesterase (AChE) contains a cluster of four conserved aspartates that can strongly bind divalent cations, which we named the 4D motif. Binding of the divalent metal cations greatly increases its thermal stability. Here we systematically examined all available crystallographic structures of T. ca...

Burkholderia pseudomallei is the causative agent of the lethal disease melioidosis. This bacterium infects animals and humans and is increasingly resistant to multiple antibiotics. Recently, genes associated with survival of the bacterium in the infected host have been identified. One of these genes, bpsl0741, is annotated as a hypothetical protein...

Looking to prevent future outbreaks of deadly pathogens by early detection? Infectious diseases continue to be a challenge that necessitates increased precision in detection and integration to achieve accurate diagnosis at the point of care (PoC). Field-effect transistors (FETs) have been investigated widely as biosensors for pathogen detection, wi...

The discovery of lytic polysaccharide monooxygenases (LPMOs), a family of copper-dependent enzymes that play a major role in polysaccharide degradation, has revealed the importance of oxidoreductases in the biological utilization of biomass. In fungi, a range of redox proteins have been implicated as working in harness with LPMOs to bring about pol...

Potassium ions ( ) are crucial for many physiological processes. Here we report on the use of a titanium dioxide (TiO2) extended gate field effect transistor as an ion sensor (ISEGFET). We tested within its critical concentration range in artificial blood serum for this. The TiO2 thin films were prepared via a solvothermal process over the conducti...

Glaciozyma antarctica PI12 is a psychrophilic yeast isolated from Antarctica. In this work, we describe the heterologous production, biochemical properties and in silico structure analysis of an arginase from this yeast (GaArg). GaArg is a metalloenzyme that catalyses the hydrolysis of l-arginine to l-ornithine and urea. The cDNA of GaArg was rever...

Gallium oxide (Ga2O3) is an ultrawide-bandgap semiconductor material that has gained attention in recent years owing to its potential applications in optoelectronic devices. Ga2O3 has become a potential material for high-performance solar-blind ultraviolet (UV–C) photodetectors in the wavelength range of 200–280 nm. One of its emerging applications...

Burkholderia pseudomallei is a highly versatile pathogen with ~25% of its genome annotated to encode hypothetical proteins. One such hypothetical protein, BPSL1038, is conserved across seven bacterial genera and 654 Burkholderia spp. Here, we present a 1.55 Å resolution crystal structure of BPSL1038. The overall structure folded into a modified βαβ...

Burkholderia pseudomallei, a soil and water saprophyte, is responsible for the tropical human disease melioidosis. A hundred years since its discovery, there is still much to learn about B. pseudomallei proteins that are essential for the bacterium's survival in and interaction with the infected host, as well as their roles within the bacterium's n...

The angiosperm Rafflesia exhibits a unique biology, including a growth strategy that involves endophytic parasitism of a specific host, with only the gigantic flower externally visible. The Rafflesia possesses many unique evolutionary, developmental, and morphological features that are rooted in yet to be explained physiological processes. Although...

The incidence of melioidosis cases caused by the gram-negative pathogen Burkholderia pseudomallei (BP) is seeing an increasing trend that has spread beyond its previously known endemic regions. Biofilms produced by BP have been associated with antimicrobial therapy limitation and relapse melioidosis, thus making it urgently necessary to understand...

The endoplasmic reticulum (ER) is a multi-layered organelle that is essential for the synthesis, folding, and structural maturation of almost one-third of the cellular proteome. It houses several resident proteins for these functions including the 21 members of the protein disulfide isomerase (PDI) family. The signature of proteins belonging to thi...

Burkholderia Lethal Factor 1 (BLF1) is a deamidase first characterized in Burkholderia pseudomallei. This enzyme inhibits cellular protein synthesis by deamidating a glutamine residue to a glutamic acid in its target protein, the eukaryotic translation initiation factor 4 A (eIF4A). In this work, we present the characterization of a hypothetical pr...

The GrAfSS (Graph theoretical Applications for Substructure Searching) webserver is a platform to search for three-dimensional substructures of: (i) amino acid side chains in protein structures; and (ii) base arrangements in RNA structures. The webserver interfaces the functions of five different graph theoretical algorithms - ASSAM, SPRITE, IMAAAG...

Burkholderiapseudomallei lethal factor 1 (BLF1) exhibits site-specific glutamine deamidase activity against the eukaryotic RNA helicase, eIF4A, thereby blocking mammalian protein synthesis. The structure of a complex between BLF1 C94S and human eIF4A shows that the toxin binds in the cleft between the two RecA-like eIF4A domains forming interaction...

The increasing number and complexity of structures containing RNA chains in the Protein Data Bank (PDB) have led to the need for automated structure annotation methods to replace or complement expert visual curation. This is especially true when searching for tertiary base motifs and substructures. Such base arrangements and motifs have diverse rol...

The glycine riboswitch is a known regulatory element that is unique in having two aptamers that are joined by a linker region. In this study, we investigated a glycine riboswitch located in the 5′ untranslated region of a glycine cleavage system homolog (gcvTHP) in Burkholderia spp. Structure prediction using the sequence generated a model with a g...

Eimeria tenella is an apicomplexan parasite that causes the economically important disease coccidiosis in chickens. An estimated loss over $3 billion USD per annum has been reported. Control of coccidiosis relies on chemotherapy and vaccination but drug resistance is common and live vaccines are relatively expensive. Therefore, there is an urgent n...

Structures of protein-drug-complexes provide an atomic level profile of drug-target interactions. In this work, the three-dimensional arrangements of amino acid side chains in known drug binding sites (substructures) were used to search for similarly arranged sites in SARS-CoV-2 protein structures in the Protein Data Bank for the potential repositi...

RNA structural motifs can be identified using methods that analyze base–base interactions and the conformation of a structure’s backbone; however, these approaches do not necessarily take into consideration the hydrogen bonds that connect the bases or the networks of inter-connected hydrogen-bonded bases that are found in RNA structures. Large clus...

The three-dimensional (3D) structures of RNA determine the functionality of the molecules. Knowledge of the functional aspects of RNA molecules from a 3D structure perspective as well as their many vital roles in various biological processes allow for applications of structural analysis such as exploring RNA structures as potential drug targets. Th...

A common drug repositioning strategy is the re-application of an existing drug to address alternative targets. A crucial aspect to enable such repurposing is that the drug's binding site on the original target is similar to that on the alternative target. Based on the assumption that proteins with similar binding sites may bind to similar drugs, th...

Background: Small open reading frames (smORF/sORFs) that encode short protein sequences are often overlooked during the standard gene prediction process thus leading to many sORFs being left undiscovered and/or misannotated. For many genomes, a second round of sORF targeted gene prediction can complement the existing annotation. In this study, we...

Parasitic plants are known to discard photosynthesis thus leading to the deletion or loss of the plastid genes. Despite plastid genome reduction in non-photosynthetic plants, some nucleus-encoded proteins are transported back to the plastid to carry out specific functions. In this work, we study such proteins in Rafflesia cantleyi, a member of the...

Introduction Computational means of assigning function have been crucial for the annotation of the numerous genomes that are being sequenced. Without a computational function annotation system, much of the genome sequences generated would remain isolated voluminous non-sensical digital outputs. The primary means of assigning a function to a new ope...

Extremely low temperatures present various challenges to life that include ice formation and effects on metabolic capacity. Psyhcrophilic microorganisms typically have an array of mechanisms to enable survival in cold temperatures. In this study, we sequenced and analysed the genome of a psychrophilic yeast isolated in the Antarctic region, Glacioz...

(Table A) Parameters for G. antarctica growth conditions (Table B) Primers used in the RT-qPCR analysis. (PDF)

The Burkholderia genus includes many species that are known to survive in diverse environmental conditions including low nutrient environments. One species, Burkholderia pseudomallei is a versatile pathogen that can survive in a wide range of hosts and environmental conditions. In this study, we investigated how a nutrient depleted growth environme...

Background Oil palm is an important source of edible oil. The importance of the crop, as well as its long breeding cycle (10-12 years) has led to the sequencing of its genome in 2013 to pave the way for genomics-guided breeding. Nevertheless, the first set of gene predictions, although useful, had many fragmented genes. Classification and character...

The advent of rapid and inexpensive DNA sequencing has led to an explosion of data that must be transformed into knowledge about genome organization and function. Gene prediction is customarily the starting point for genome analysis. This paper presents a bioinformatics study of the oil palm genome, including a comparative genomics analysis, databa...

Background Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. However, these systems have yet to accurately predict all or even most of the protein-coding regions. Furthermore, none of the cur...

Rafflesia is a biologically enigmatic species that is very rare in occurrence and possesses an extraordinary morphology. This parasitic plant produces a gigantic flower up to one metre in diameter with no leaves, stem or roots. However, little is known about the floral biology of this species especially at the molecular level. In an effort to addre...

List of transcription factor annotation for Rafflesia cantleyi flower transcripts. (XLSX)

Functional annotation of the 52 transcripts that showed very high abundance in the Rafflesia cantleyi flower transcriptome. (XLSX)

K-mer distribution plot. (TIF)

List of annotation for Rafflesia cantleyi flower transcripts. (XLSX)

Top enriched KEGG pathways represented in the Rafflesia cantleyi flower transcripts. (XLSX)

Genes differentially expressed between flower and floral bud of Rafflesia cantleyi. (XLSX)

Annotation of genes that showed higher expression in the perigone tissue of the flower compared to the floral bud of Rafflesia cantleyi. (XLSX)

List of Rafflesia cantleyi genes selected for RT-qPCR analysis. (XLSX)

List of enzyme code annotation for Rafflesia cantleyi flower transcripts. (XLSX)

Background Biological macromolecules (DNA, RNA and proteins) are capable of processing physical or chemical inputs to generate outputs that parallel conventional Boolean logical operators. However, the design of functional modules that will enable these macromolecules to operate as synthetic molecular computing devices is challenging. Results Usin...

Burkholderia pseudomallei, the causative agent of melioidosis, is among a growing number of bacterial pathogens that are increasingly antibiotic resistant. Antimicrobial peptides (AMPs) have been investigated as an alternative approach to treat microbial infections, as generally, there is a lower likelihood that a pathogen will develop resistance t...

Fabrication of functional DNA nanostructures operating at a cellular level has been accomplished through molecular programming techniques such as DNA origami and single-stranded tiles (SST). During implementation, restrictive and constraint dependent designs are enforced to ensure conformity is attainable. We propose a concept of DNA polyominoes th...

Although various software are available for gene prediction, none of the currently available gene-finders have a universal Hidden Markov Models (HMM) that can perform gene prediction for all organisms equally well in an automatic fashion. Here, we report an automated pipeline that performs gene prediction using selftrained HMM models and transcript...

Background There are still numerous protein subfamilies within families and superfamilies that do not yet have conclusive empirical experimental evidence providing a specific function. These proteins persist in databases with the annotation of a specific ‘putative’ function made by association with discernible features in the protein sequence. Res...

A major component of RNA structure stabilization are the hydrogen bonded interactions between the base residues. The importance and biological relevance for large clusters of base interactions can be much more easily investigated when their occurrences have been systematically detected, catalogued and compared. In this paper, we describe the databa...

Hypothetical proteins of bacterial pathogens represent a large numbers of novel biological mechanisms which could belong to essential pathways in the bacteria. They lack functional characterizations mainly due to the inability of sequence homology based methods to detect functional relationships in the absence of detectable sequence similarity. The...

Glaciozyma antarctica is an obligate psychrophilic yeast that was isolated from Casey Research Station, Antarctica. The objective of this study was to identify small Open Reading Frames (sORFs) in the G. antarctica genome. Small ORFs have been found in other organisms including Saccharomyces cerevisiae and human and they have been known to partake...

A cDNA encoding Fe(II) 2-oxoglutarate (2OG) dependent dioxygenases was isolated from psychrophilic yeast, Glaciozyma antarctica PI12. We have successfully amplified 1,029 bp cDNA sequence that encodes 342 amino acid with predicted molecular weight 38 kDa. The prediction protein was analysed using various bioinformatics tools to explore the properti...