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  1. Article ; Online: Protein diversification through post-translational modifications, alternative splicing, and gene duplication.

    Goldtzvik, Yonathan / Sen, Neeladri / Lam, Su Datt / Orengo, Christine

    Current opinion in structural biology

    2023  Volume 81, Page(s) 102640

    Abstract: Proteins provide the basis for cellular function. Having multiple versions of the same protein within a single organism provides a way of regulating its activity or developing novel functions. Post-translational modifications of proteins, by means of ... ...

    Abstract Proteins provide the basis for cellular function. Having multiple versions of the same protein within a single organism provides a way of regulating its activity or developing novel functions. Post-translational modifications of proteins, by means of adding/removing chemical groups to amino acids, allow for a well-regulated and controlled way of generating functionally distinct protein species. Alternative splicing is another method with which organisms possibly generate new isoforms. Additionally, gene duplication events throughout evolution generate multiple paralogs of the same genes, resulting in multiple versions of the same protein within an organism. In this review, we discuss recent advancements in the study of these three methods of protein diversification and provide illustrative examples of how they affect protein structure and function.
    MeSH term(s) Alternative Splicing ; Gene Duplication ; Evolution, Molecular ; Protein Isoforms/genetics ; Protein Processing, Post-Translational
    Chemical Substances Protein Isoforms
    Language English
    Publishing date 2023-06-23
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1068353-7
    ISSN 1879-033X ; 0959-440X
    ISSN (online) 1879-033X
    ISSN 0959-440X
    DOI 10.1016/j.sbi.2023.102640
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article: Curcumin and Its Derivatives as Potential Antimalarial and Anti-Inflammatory Agents: A Review on Structure-Activity Relationship and Mechanism of Action.

    Jamil, Siti Nur Hidayah / Ali, Amatul Hamizah / Feroz, Shevin Rizal / Lam, Su Datt / Agustar, Hani Kartini / Mohd Abd Razak, Mohd Ridzuan / Latip, Jalifah

    Pharmaceuticals (Basel, Switzerland)

    2023  Volume 16, Issue 4

    Abstract: Curcumin, one of the major ingredients of turmeric ( ...

    Abstract Curcumin, one of the major ingredients of turmeric (
    Language English
    Publishing date 2023-04-18
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2193542-7
    ISSN 1424-8247
    ISSN 1424-8247
    DOI 10.3390/ph16040609
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  3. Article: Identification of Potential Genes Encoding Protein Transporters in

    Harun, Sarahani / Afiqah-Aleng, Nor / Abdul Hadi, Fatin Izzati / Lam, Su Datt / Mohamed-Hussein, Zeti-Azura

    Life (Basel, Switzerland)

    2022  Volume 12, Issue 3

    Abstract: Several species ... ...

    Abstract Several species in
    Language English
    Publishing date 2022-02-22
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2662250-6
    ISSN 2075-1729
    ISSN 2075-1729
    DOI 10.3390/life12030326
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  4. Article: Structural and energetic analyses of SARS-CoV-2

    Lam, Su Datt / Waman, Vaishali P / Fraternali, Franca / Orengo, Christine / Lees, Jonathan

    Computational and structural biotechnology journal

    2022  Volume 20, Page(s) 6302–6316

    Abstract: Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged affecting transmissibility, disease severity and re-infection risk. Studies ... ...

    Abstract Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 is an ongoing pandemic that causes significant health/socioeconomic burden. Variants of concern (VOCs) have emerged affecting transmissibility, disease severity and re-infection risk. Studies suggest that the -
    Language English
    Publishing date 2022-11-07
    Publishing country Netherlands
    Document type Journal Article
    ZDB-ID 2694435-2
    ISSN 2001-0370
    ISSN 2001-0370
    DOI 10.1016/j.csbj.2022.11.004
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  5. Article ; Online: Biological impact of mutually exclusive exon switching.

    Lam, Su Datt / Babu, M Madan / Lees, Jonathan / Orengo, Christine A

    PLoS computational biology

    2021  Volume 17, Issue 3, Page(s) e1008708

    Abstract: Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch ... ...

    Abstract Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem.ucl.ac.uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.
    MeSH term(s) Alternative Splicing/genetics ; Animals ; Evolution, Molecular ; Exons/genetics ; Genome/genetics ; Genomics ; Humans ; Proteins/genetics ; Proteins/physiology
    Chemical Substances Proteins
    Language English
    Publishing date 2021-03-02
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2193340-6
    ISSN 1553-7358 ; 1553-734X
    ISSN (online) 1553-7358
    ISSN 1553-734X
    DOI 10.1371/journal.pcbi.1008708
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Biological impact of mutually exclusive exon switching.

    Su Datt Lam / M Madan Babu / Jonathan Lees / Christine A Orengo

    PLoS Computational Biology, Vol 17, Iss 3, p e

    2021  Volume 1008708

    Abstract: Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch ... ...

    Abstract Alternative splicing can expand the diversity of proteomes. Homologous mutually exclusive exons (MXEs) originate from the same ancestral exon and result in polypeptides with similar structural properties but altered sequence. Why would some genes switch homologous exons and what are their biological impact? Here, we analyse the extent of sequence, structural and functional variability in MXEs and report the first large scale, structure-based analysis of the biological impact of MXE events from different genomes. MXE-specific residues tend to map to single domains, are highly enriched in surface exposed residues and cluster at or near protein functional sites. Thus, MXE events are likely to maintain the protein fold, but alter specificity and selectivity of protein function. This comprehensive resource of MXE events and their annotations is available at: http://gene3d.biochem.ucl.ac.uk/mxemod/. These findings highlight how small, but significant changes at critical positions on a protein surface are exploited in evolution to alter function.
    Keywords Biology (General) ; QH301-705.5
    Subject code 612
    Language English
    Publishing date 2021-03-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: AlphaFold2 reveals commonalities and novelties in protein structure space for 21 model organisms

    Nicola Bordin / Ian Sillitoe / Vamsi Nallapareddy / Clemens Rauer / Su Datt Lam / Vaishali P. Waman / Neeladri Sen / Michael Heinzinger / Maria Littmann / Stephanie Kim / Sameer Velankar / Martin Steinegger / Burkhard Rost / Christine Orengo

    Communications Biology, Vol 6, Iss 1, Pp 1-

    2023  Volume 12

    Abstract: A new protein domain classification protocol incorporating deep learning strategies for detecting sequence and structure similarities between domain is used to systematically study and analyse the predicted AlphaFold2 structural models for proteins of 21 ...

    Abstract A new protein domain classification protocol incorporating deep learning strategies for detecting sequence and structure similarities between domain is used to systematically study and analyse the predicted AlphaFold2 structural models for proteins of 21 organisms.
    Keywords Biology (General) ; QH301-705.5
    Language English
    Publishing date 2023-02-01T00:00:00Z
    Publisher Nature Portfolio
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  8. Article: Proteomics and Interspecies Interaction Analysis Revealed Abscisic Acid Signalling to Be the Primary Driver for Oil Palm's Response against Red Palm Weevil Infestation.

    Harith-Fadzilah, Nazmi / Lam, Su Datt / Haris-Hussain, Mohammad / Ghani, Idris Abd / Zainal, Zamri / Jalinas, Johari / Hassan, Maizom

    Plants (Basel, Switzerland)

    2021  Volume 10, Issue 12

    Abstract: The red palm weevil (RPW; ...

    Abstract The red palm weevil (RPW;
    Language English
    Publishing date 2021-11-25
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2704341-1
    ISSN 2223-7747
    ISSN 2223-7747
    DOI 10.3390/plants10122574
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  9. Article ; Online: Identification of Potential Genes Encoding Protein Transporters in Arabidopsis thaliana Glucosinolate (GSL) Metabolism

    Sarahani Harun / Nor Afiqah-Aleng / Fatin Izzati Abdul Hadi / Su Datt Lam / Zeti-Azura Mohamed-Hussein

    Life, Vol 12, Iss 326, p

    2022  Volume 326

    Abstract: Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana , the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and ... ...

    Abstract Several species in Brassicaceae produce glucosinolates (GSLs) to protect themselves against pests. As demonstrated in A. thaliana , the reallocation of defence compounds, of which GSLs are a major part, is highly dependent on transport processes and serves to protect high-value tissues such as reproductive tissues. This study aimed to identify potential GSL-transporter proteins (TPs) using a network-biology approach. The known A. thaliana GSL genes were retrieved from the literature and pathway databases and searched against several co-expression databases to generate a gene network consisting of 1267 nodes and 14,308 edges. In addition, 1151 co-expressed genes were annotated, integrated, and visualised using relevant bioinformatic tools. Based on three criteria, 21 potential GSL genes encoding TPs were selected. The AST68 and ABCG40 potential GSL TPs were chosen for further investigation because their subcellular localisation is similar to that of known GSL TPs (SULTR1;1 and SULTR1;2) and ABCG36, respectively. However, AST68 was selected for a molecular-docking analysis using AutoDOCK Vina and AutoDOCK 4.2 with the generated 3D model, showing that both domains were well superimposed on the homologs. Both molecular-docking tools calculated good binding-energy values between the sulphate ion and Ser419 and Val172, with the formation of hydrogen bonds and van der Waals interactions, respectively, suggesting that AST68 was one of the sulphate transporters involved in GSL biosynthesis. This finding illustrates the ability to use computational analysis on gene co-expression data to screen and characterise plant TPs on a large scale to comprehensively elucidate GSL metabolism in A. thaliana . Most importantly, newly identified potential GSL transporters can serve as molecular tools in improving the nutritional value of crops.
    Keywords glucosinolate ; co-expression network ; molecular docking ; transporter proteins ; Science ; Q
    Subject code 580
    Language English
    Publishing date 2022-02-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  10. Article ; Online: Machine learning and molecular simulation ascertain antimicrobial peptide against Klebsiella pneumoniae from public database.

    Al-Khdhairawi, Ahmad / Sanuri, Danish / Akbar, Rahmad / Lam, Su Datt / Sugumar, Shobana / Ibrahim, Nazlina / Chieng, Sylvia / Sairi, Fareed

    Computational biology and chemistry

    2022  Volume 102, Page(s) 107800

    Abstract: Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of ... ...

    Abstract Antimicrobial peptides (AMPs) are short peptides with a broad spectrum of antimicrobial activity. They play a key role in the host innate immunity of many organisms. The growing threat of microorganisms resistant to antimicrobial agents and the lack of new commercially available antibiotics have made in silico discovery of AMPs increasingly important. Machine learning (ML) has improved the speed and efficiency of AMP discovery while reducing the cost of experimental approaches. Despite various ML platforms developed, there is still a lack of integrative use of ML platforms for AMP discovery from publicly available protein databases. Therefore, our study aims to screen potential AMPs with antibiofilm properties from databases using ML platforms, followed by protein-peptide molecular docking analysis and molecular dynamics (MD) simulations. A total of 5850 peptides classified as non-AMP were screened from UniProtKB and analyzed using various online ML platforms (e.g., CAMPr3, DBAASP, dPABBs, Hemopred, and ToxinPred). Eight potential AMP peptides against Klebsiella pneumoniae with antibiofilm, non-toxic and non-hemolytic properties were then docked to MrkH, a transcriptional regulator of type 3 fimbriae involved in biofilm formation. Five of eight peptides bound more strongly than the native MrkH ligand when analyzed using HADDOCK and HPEPDOCK. Following the docking studies, our MD simulated that a Neuropeptide B (Peptide 3) bind strongly to the MrkH active sites. The discovery of putative AMPs that exceed the binding energies of the native ligand underscores the utility of the combined ML and molecular simulation strategies for discovering novel AMPs with antibiofilm properties.
    MeSH term(s) Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/metabolism ; Antimicrobial Peptides/pharmacology ; Klebsiella pneumoniae/drug effects ; Ligands ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Machine Learning
    Chemical Substances Anti-Bacterial Agents ; Antimicrobial Peptides ; Ligands
    Language English
    Publishing date 2022-12-05
    Publishing country England
    Document type Journal Article
    ISSN 1476-928X
    ISSN (online) 1476-928X
    DOI 10.1016/j.compbiolchem.2022.107800
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