Institute of Molecular science and Bioinformatics

Lahore, Pakistan

Institute of Molecular science and Bioinformatics

Lahore, Pakistan
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Hussain M.R.M.,Institute of Molecular science and Bioinformatics | Hussain M.R.M.,King Abdulaziz University | Hassan M.,Brunel University | Iqbal Z.,Institute of Molecular science and Bioinformatics
Central European Journal of Medicine | Year: 2012

According to the universal biological findings, cellular bodies are covered with an intense coating of glycans. Diversity of glycan chains, linked to lipids and proteins is due to isomeric and conformational modifications of various sugar residues, giving rise to unique carbohydrate structures with a wide range of sequences and anomeric configurations. Proteins and lipids, carrying specific sugar residues (like Galactose) with particular stereochemical properties (sequence, anomery and linkages) are involved in broad spectrums of biological processes, including intercellular and intracellular interactions, microbial adhesion and cellular signaling. By studying the role of specific seterochemical features of galactose (Gal), we have improved our understanding about the normal physiology and diseases in human bodies. © Versita Sp. z o.o.


Din N.U.,Institute of Molecular science and Bioinformatics | Din N.U.,University of Karachi | Ahmad I.,Institute of Molecular science and Bioinformatics | Haq I.U.,The University of Lahore | And 3 more authors.
Journal of Cellular Biochemistry | Year: 2010

Long-term potentiation (LTP) and long-term depression (LTD) are the current models of synaptic plasticity and widely believed to explain how different kinds of memory are stored in different brain regions. Induction of LTP and LTD in different regions of brain undoubtedly involve trafficking of AMPA receptor to and from synapses. Hippocampal LTP involves phosphorylation of GluR1 subunit of AMPA receptor and its delivery to synapse whereas; LTD is the result of dephosphorylation and endocytosis of GluR1 containing AMPA receptor. Conversely the cerebellar LTD is maintained by the phosphorylation of GluR2 which promotes receptor endocytosis while dephosphorylation of GluR2 triggers receptor expression at the cell surface and results in LTP. The interplay of phosphorylation and O-GlcNAc modification is known as functional switch in many neuronal proteins. In this study it is hypothesized that a same phenomenon underlies as LTD and LTP switching, by predicting the potential of different Ser/Thr residues for phosphorylation, O-GlcNAc modification and their possible interplay. We suggest the involvement of O-GlcNAc modification of dephosphorylated GluR1 in maintaining the hippocampal LTD and that of dephosphorylated GluR2 in cerebral LTP. © 2010 Wiley-Liss, Inc.


Iqbal Z.,Institute of Molecular science and Bioinformatics | Hoessli D.C.,Institute of Molecular science and Bioinformatics | Hoessli D.C.,University of Karachi | Kaleem A.,Institute of Molecular science and Bioinformatics | And 7 more authors.
Journal of Cellular Biochemistry | Year: 2013

Proteins function is regulated by co-translational modifications and post-translational modifications (PTMs) such as phosphorylation, glycosylation, and acetylation, which induce proteins to perform multiple tasks in a specified environment. Acetylation takes place post-translationally on the ε-amino group of Lys in histone proteins, allowing regulation of gene expression. Furthermore, amino group acetylation also occurs co-translationally on Ser, Thr, Gly, Met, and Ala, possibly contributing to the stability of proteins. In this work, the influence of amino acids next to acetylated sites has been investigated by using MAPRes (Mining Association Patterns among preferred amino acid residues in the vicinity of amino acids targeted for PTMs). MAPRes was utilized to examine the sequence patterns vicinal to modified and non-modified residues, taking into account their charge and polarity. The PTMs data were further sub-divided according to their sub-cellular location (nuclear, mitochondrial, and cytoplasmic), and their association patterns were mined. The association patterns mined by MAPRes for acetylated and non-acetylated residues are consistent with the existing literature but also revealed novel patterns. These rules have been utilized to describe the acetylation and its effects on the protein structure-function relationship. J. Cell. Biochem. 114: 874-887, 2013. © 2012 Wiley Periodicals, Inc. Copyright © 2012 Wiley Periodicals, Inc.


Shakoori A.R.,University of Punjab | Hoessli D.C.,Institute of Molecular science and Bioinformatics | Nasir-Ud-Din,Institute of Molecular science and Bioinformatics | Nasir-Ud-Din,University of Karachi
Journal of Cellular Biochemistry | Year: 2013

Octamer DNA binding transcription factors play important roles in housekeeping and specific gene regulations. Octamer DNA binding transcription factor-1 (Oct-1), expressed ubiquitously, is a multifunctional molecule. The binding sites of Oct-1 are the promoters of H2B gene and the genes of snRNA, U2, U6, and 7SK, yet Oct-1 has been described as constitutively expressed transcription factor regulating the expression of housekeeping genes. Diverse tissue-specific genes regulations by Oct-1 include genes for interleukins (IL) 2, 3, 5; the granulocyte-macrophagal colony-stimulating factor, immunoglobulins α, β, Ly9; the endocrine-associated Pit-1 gene; the genes for gonadoliberin, prolactin, the thyroid transcription factor, and thyrotropin. The most interesting aspect of the gene regulations of Oct-1 includes both activation and inhibition of transcription. These opposite regulations of Oct-1 have been described through presence/absence of a post-translational modification (PTM) in its different domains. We propose a mechanism of interplay of different PTMs or presence/absence of PTMs in the different domains of Oct-1. We also suggest that the absence of phosphorylation and acetylation in G1 and S phases of the cell cycle is associated with interplay of methylation and O-GlcNAc modification. This interplay of O-GlcNAc modification with the phosphorylation and methylation with acetylation in POU sub-domain of Oct-1 may facilitate the formation of Oct-1-DNA complex, consequently activating H2B gene transcription. Whereas, in G2 and M phases these sites are occupied by phosphate resulting in inhibition of Oct-1-DNA complex formation leading to the suppression of H2B gene transcription. © 2012 Wiley Periodicals, Inc.


Kaleem A.,Institute of Molecular science and Bioinformatics | Kaleem A.,The University of Lahore | Hoessli D.C.,Institute of Molecular science and Bioinformatics | Hoessli D.C.,University of Karachi | And 8 more authors.
Journal of Cellular Biochemistry | Year: 2011

The multifunctionality of proteins is dictated by post-translational modifications (PTMs) which involve the attachment of small functional groups such as phosphate and acetate, as well as carbohydrate moieties. These functional groups make the protein perform various functions in different environments. PTMs play a crucial role in memory and learning. Phosphorylation of synaptic proteins and transcription factors regulate the generation and storage of memory. Among these is the cAMP-regulated element binding protein CREB that regulates CRE containing genes like c-fos. Both phosphorylation and acetylation control the function of CREB as a transcription factor. CREB is also susceptible to O-GlcNAc modification, which inhibits its activity. O-GlcNAc modification occurs on the same or neighboring Ser/Thr residues akin to phosphorylation. An interplay between these modifications was shown to operate in nuclear and cytoplasmic proteins. In this study computational methods were utilized to predict different modification sites in CREB. These in silico results suggest that phosphorylation, OGlcNAc modification and acetylation modulate the transcriptional activity of CREB and thus dictate its contribution to synaptic plasticity. J. Cell. © 2010 Wiley-Liss, Inc.


Hussain M.R.M.,Institute of Molecular science and Bioinformatics | Hassan M.,University of Punjab | Hassan M.,Brunel University | Afzal I.,Institute of Molecular science and Bioinformatics | Afzal A.,University of Punjab
Egyptian Journal of Medical Human Genetics | Year: 2012

Glycoconjugates are involved in the vital physiological functions including blood group determination, cancer recognition, protein stabilization, sperm-egg adhesion and pathogenic interaction in the body. These diverse biological functions of glycoconjugates are regulated by complex oligosaccharide structures linked with proteins and lipids in macromolecular assemblies. The diversity in oligosaccharide chains attached with lipids and proteins is specifically linked with the conformational behavior of sugar residues giving rise to unique carbohydrate structures with a wide range of sequence and anomeric linkages. This is a challenging task to explore the relationship between biological processes and stereochemical behavior of sugar residues. Current review article focuses the specific stereochemical involvement (anomery and linkages) of Gal and its derivative GalNAc in a wide range of cellular activities. These sugar residues exhibit different physiological functions at the terminal and subterminal positions in glycans. © 2012 Production and hosting by Elsevier B.V.


Iqbal Z.,Institute of Molecular science and Bioinformatics | Hoessli D.C.,Institute of Molecular science and Bioinformatics | Hoessli D.C.,University of Karachi | Qazi W.M.,The University of Lahore | And 4 more authors.
Journal of Cellular Biochemistry | Year: 2015

Several models that predict where post-translational modifications are likely to occur and formulate the corresponding association rules are available to analyze the functional potential of a protein sequence, but an algorithm incorporating the functional groups of the involved amino acids in the sequence analyses process is not yet available. In its previous version, MAPRes was utilized to investigate the influence of the surrounding amino acids of post- translationally and co-translationally modifiable sites. The MAPRes has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post- translational modifications (PTMs). In the present study, the upgraded version of MAPRes was implemented on phosphorylated Ser/Thr/Tyr data by considering the polarity and charge of the surrounding amino acids. The patterns mined by MAPRes incorporating structural information on polarity and charge of amino acids suggest distinct structure-function relationships for phosphorylated serines in a multifunctional protein such as the insulin-receptor substrate-1 (IRS-1) protein. The new version of MAPRes is freely available at http://www.imsb.edu.pk/Database.htm. J. Cell. Biochem. 116: 370-379, 2015. © 2014 Wiley Periodicals, Inc.


PubMed | Institute of Molecular science and Bioinformatics
Type: Journal Article | Journal: Journal of cellular biochemistry | Year: 2013

Proteins function is regulated by co-translational modifications and post-translational modifications (PTMs) such as phosphorylation, glycosylation, and acetylation, which induce proteins to perform multiple tasks in a specified environment. Acetylation takes place post-translationally on the -amino group of Lys in histone proteins, allowing regulation of gene expression. Furthermore, amino group acetylation also occurs co-translationally on Ser, Thr, Gly, Met, and Ala, possibly contributing to the stability of proteins. In this work, the influence of amino acids next to acetylated sites has been investigated by using MAPRes (Mining Association Patterns among preferred amino acid residues in the vicinity of amino acids targeted for PTMs). MAPRes was utilized to examine the sequence patterns vicinal to modified and non-modified residues, taking into account their charge and polarity. The PTMs data were further sub-divided according to their sub-cellular location (nuclear, mitochondrial, and cytoplasmic), and their association patterns were mined. The association patterns mined by MAPRes for acetylated and non-acetylated residues are consistent with the existing literature but also revealed novel patterns. These rules have been utilized to describe the acetylation and its effects on the protein structure-function relationship.


PubMed | Institute of Molecular science and Bioinformatics
Type: Journal Article | Journal: Journal of cellular biochemistry | Year: 2010

Long-term potentiation (LTP) and long-term depression (LTD) are the current models of synaptic plasticity and widely believed to explain how different kinds of memory are stored in different brain regions. Induction of LTP and LTD in different regions of brain undoubtedly involve trafficking of AMPA receptor to and from synapses. Hippocampal LTP involves phosphorylation of GluR1 subunit of AMPA receptor and its delivery to synapse whereas; LTD is the result of dephosphorylation and endocytosis of GluR1 containing AMPA receptor. Conversely the cerebellar LTD is maintained by the phosphorylation of GluR2 which promotes receptor endocytosis while dephosphorylation of GluR2 triggers receptor expression at the cell surface and results in LTP. The interplay of phosphorylation and O-GlcNAc modification is known as functional switch in many neuronal proteins. In this study it is hypothesized that a same phenomenon underlies as LTD and LTP switching, by predicting the potential of different Ser/Thr residues for phosphorylation, O-GlcNAc modification and their possible interplay. We suggest the involvement of O-GlcNAc modification of dephosphorylated GluR1 in maintaining the hippocampal LTD and that of dephosphorylated GluR2 in cerebral LTP.


PubMed | Institute of Molecular science and Bioinformatics
Type: Journal Article | Journal: Journal of cellular biochemistry | Year: 2015

Several models that predict where post-translational modifications are likely to occur and formulate the corresponding association rules are available to analyze the functional potential of a protein sequence, but an algorithm incorporating the functional groups of the involved amino acids in the sequence analyses process is not yet available. In its previous version, MAPRes was utilized to investigate the influence of the surrounding amino acids of post- translationally and co-translationally modifiable sites. The MAPRes has been upgraded to take into account the different biophysical and biochemical properties of the amino acids that have the potential to influence different post- translational modifications (PTMs). In the present study, the upgraded version of MAPRes was implemented on phosphorylated Ser/Thr/Tyr data by considering the polarity and charge of the surrounding amino acids. The patterns mined by MAPRes incorporating structural information on polarity and charge of amino acids suggest distinct structure-function relationships for phosphorylated serines in a multifunctional protein such as the insulin-receptor substrate-1 (IRS-1) protein. The new version of MAPRes is freely available at http://www.imsb.edu.pk/Database.htm.

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