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  1. Article ; Online: Be

    Sabu, Gopika / De, Susmita

    The journal of physical chemistry. B

    2023  Volume 127, Issue 48, Page(s) 10326–10337

    Abstract: Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the ... ...

    Abstract Although the ion selectivity of metalloproteins has been well established, selective metal antigen recognition by immunoproteins remains elusive. One such case is the recognition of the Be
    MeSH term(s) Humans ; Binding Sites ; Metals/chemistry ; Peptides/metabolism ; Ions/chemistry ; Metalloproteins/metabolism
    Chemical Substances Metals ; Peptides ; Ions ; Metalloproteins
    Language English
    Publishing date 2023-11-27
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.3c05461
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: Cation-π and hydrophobic interaction controlled PET recognition in double mutated cutinase - identification of a novel binding subsite for better catalytic activity.

    James, Anjima / De, Susmita

    RSC advances

    2022  Volume 12, Issue 32, Page(s) 20563–20577

    Abstract: Accelerated hydrolysis of polyethylene terephthalate (PET) by enzymatic surface modification of various hydrolases, which would not degrade the building blocks of PET in order to retain the quality of recycled PET, is a promising research area. Many ... ...

    Abstract Accelerated hydrolysis of polyethylene terephthalate (PET) by enzymatic surface modification of various hydrolases, which would not degrade the building blocks of PET in order to retain the quality of recycled PET, is a promising research area. Many studies have been reported to identify mutations of different hydrolases that can improve PET degradation. Recently, the mutation of glycine and phenyl alanine with alanine in cutinase was found to improve the activity of PET degradation 6-fold. Yet, a deep insight into the overall structural basis as well as the explicit role played by the amino acid residues for PET degradation is still elusive, which is nevertheless important for comparative analyses, structure-function relations and rational optimization of the degradation process. Our molecular dynamics simulations coupled with quantum mechanical study demonstrate that mutations of anchor residue phenyl alanine to alanine at the PET binding cleft of cutinase unveiled a distal yet novel binding subsite, which alters the nature of dispersive interaction for PET recognition and binding. The phenyl alanine engages in π-π interaction with the phenyl ring of PET (-8.5 kcal mol
    Language English
    Publishing date 2022-07-15
    Publishing country England
    Document type Journal Article
    ISSN 2046-2069
    ISSN (online) 2046-2069
    DOI 10.1039/d2ra03394a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article: Cation–π and hydrophobic interaction controlled PET recognition in double mutated cutinase – identification of a novel binding subsite for better catalytic activity

    James, Anjima / De, Susmita

    RSC advances. 2022 July 15, v. 12, no. 32

    2022  

    Abstract: Accelerated hydrolysis of polyethylene terephthalate (PET) by enzymatic surface modification of various hydrolases, which would not degrade the building blocks of PET in order to retain the quality of recycled PET, is a promising research area. Many ... ...

    Abstract Accelerated hydrolysis of polyethylene terephthalate (PET) by enzymatic surface modification of various hydrolases, which would not degrade the building blocks of PET in order to retain the quality of recycled PET, is a promising research area. Many studies have been reported to identify mutations of different hydrolases that can improve PET degradation. Recently, the mutation of glycine and phenyl alanine with alanine in cutinase was found to improve the activity of PET degradation 6-fold. Yet, a deep insight into the overall structural basis as well as the explicit role played by the amino acid residues for PET degradation is still elusive, which is nevertheless important for comparative analyses, structure–function relations and rational optimization of the degradation process. Our molecular dynamics simulations coupled with quantum mechanical study demonstrate that mutations of anchor residue phenyl alanine to alanine at the PET binding cleft of cutinase unveiled a distal yet novel binding subsite, which alters the nature of dispersive interaction for PET recognition and binding. The phenyl alanine engages in π–π interaction with the phenyl ring of PET (−8.5 kcal mol⁻¹), which on one side helps in PET recognition, but on the other side restricts PET to attain fully extended conformations over the entire binding cleft. The loss of π–π interaction due to mutation of phenyl alanine to alanine is not only compensated by the favourable cation–π and hydrophobic interactions from the arginine residues (−17.1 kcal mol⁻¹) found in the newly discovered subsite, but also favours the fully extended PET conformation. This subsequently impacts the overall increased catalytic activity of mutated cutinase.
    Keywords alanine ; arginine ; catalytic activity ; cutinase ; hydrolysis ; hydrophobic bonding ; hydrophobicity ; molecular dynamics ; mutation ; polyethylene terephthalates ; quantum mechanics
    Language English
    Dates of publication 2022-0715
    Size p. 20563-20577.
    Publishing place The Royal Society of Chemistry
    Document type Article
    ISSN 2046-2069
    DOI 10.1039/d2ra03394a
    Database NAL-Catalogue (AGRICOLA)

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  4. Article ; Online: Dual-Site Binding of Quaternary Ammonium Ions as Internal K

    Cholasseri, Rinsha / De, Susmita

    The journal of physical chemistry. B

    2020  Volume 125, Issue 1, Page(s) 86–100

    Abstract: A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA ... ...

    Abstract A molecular-level study of the influence of the alkyl chain length of quaternary ammonium ions (QAs) on the blocking action and the mode of binding with the bacterial KcsA K
    Language English
    Publishing date 2020-12-28
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ISSN 1520-5207
    ISSN (online) 1520-5207
    DOI 10.1021/acs.jpcb.0c09604
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: Hydrogen Evolution Activity of Nitrogen-Rich

    Rajendramani, Radha / Madan, Krateeka / Kallingal, Mohammed Sadik Nalakath / Guru, Sruthi / De, Susmita / Gangavarapu, Ranga Rao

    Langmuir : the ACS journal of surfaces and colloids

    2023  Volume 39, Issue 34, Page(s) 11992–12003

    Abstract: Synthesis of a metal-free carbon nitride ( ...

    Abstract Synthesis of a metal-free carbon nitride (
    Language English
    Publishing date 2023-08-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2005937-1
    ISSN 1520-5827 ; 0743-7463
    ISSN (online) 1520-5827
    ISSN 0743-7463
    DOI 10.1021/acs.langmuir.3c00867
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article ; Online: Site-selective post-modification of short α/γ hybrid foldamers: a powerful approach for molecular diversification towards biomedical applications.

    Shah, Syed Kabir Hussain / Modi, Unnati / Patel, Karma / James, Anjima / N, Sreerag / De, Susmita / Vasita, Rajesh / Prabhakaran, Panchami

    Biomaterials science

    2023  Volume 11, Issue 18, Page(s) 6210–6222

    Abstract: The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification ... ...

    Abstract The extensive research work in the exhilarating area of foldamers (artificial oligomers possessing well-defined conformation in solution) has shown them to be promising candidates in biomedical research and materials science. The post-modification approach is successful in peptides, proteins, and polymers to modulate their functions. To the best of our knowledge, site-selective post-modification of a foldamer affording molecules with different pendant functional groups within a molecular scaffold has not yet been reported. We demonstrate for the first time that late-stage site-selective functionalization of short hybrid oligomers is an efficient approach to afford molecules with diverse functional groups. In this article, we report the design and synthesis of hybrid peptides with repeating units of leucine (Leu) and 5-amino salicylic acid (ASA), regioselective post-modification, conformational analyses (based on solution-state NMR, circular dichroism and computational studies) and morphological studies of the peptide nanostructures. As a proof-of-concept, we demonstrate the applications of differently modified peptides as drug delivery agents, imaging probes, and anticancer agents. The novel feature of the work is that the difference in reactivity of two phenolic OH groups in short biomimetic peptides was utilized to achieve site-selective post-modification. It is challenging to apply the same approach to short α-peptides having a poor folding tendency, and their post-functionalization may considerably affect their conformation.
    MeSH term(s) Peptides/chemistry ; Proteins ; Molecular Conformation ; Magnetic Resonance Spectroscopy
    Chemical Substances Peptides ; Proteins
    Language English
    Publishing date 2023-09-12
    Publishing country England
    Document type Journal Article
    ZDB-ID 2693928-9
    ISSN 2047-4849 ; 2047-4830
    ISSN (online) 2047-4849
    ISSN 2047-4830
    DOI 10.1039/d3bm00766a
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  7. Article ; Online: Molecular mechanism of Be

    De, Susmita / Sabu, Gopika / Zacharias, Martin

    Physical chemistry chemical physics : PCCP

    2019  Volume 22, Issue 2, Page(s) 799–810

    Abstract: The chemistry of beryllium is rather unusual, however, less explored as compared to other main group elements. This is mainly attributed to the high toxicity of beryllium, leading to chronic granulomatous pneumonitis, called chronic beryllium disease ( ... ...

    Abstract The chemistry of beryllium is rather unusual, however, less explored as compared to other main group elements. This is mainly attributed to the high toxicity of beryllium, leading to chronic granulomatous pneumonitis, called chronic beryllium disease (CBD). It has been reported that Be2+-ion binding to the human leukocyte antigen protein (HLA-DP2) and peptide (M2) results in favorable interaction with the T-cell receptor protein (TCR), which initiates immune-mediated toxicity. We have carried out molecular dynamics (MD) simulations combined with quantum mechanical/molecular mechanical (QM/MM) studies to explore the binding nature of Be2+ with a HLA-DP2 protein and M2 peptide. The interaction between the negatively charged M2 peptide and the negatively charged binding cleft of HLA-DP2 is unfavorable. However, this interaction is stabilized by one Be2+ and two Na+-ions bridged by negatively charged carboxyl groups of glutamate residues (β26E and β69E) of the β-chain of HLA-DP2 and one glutamate (p7E) and one aspartate residue (p4D) of the M2 peptide. This multi-ion cavity consists of tetrahedrally coordinated static Be2+ and Na+-ions, as well as one dynamically exchangeable Na+-ion. The smaller size and higher charge of the Be2+-ion as compared to the Na+-ion reduce the distance between the M2 peptide and the β-chain of HLA-DP2, which results in conformational change suitable for TCR binding. However, the replacement of the Be2+ by the Na+-ion could not generate a suitable binding site for TCR.
    MeSH term(s) Beryllium/chemistry ; Binding Sites ; HLA-DP beta-Chains/chemistry ; Humans ; Ions/chemistry ; Models, Molecular ; Molecular Conformation
    Chemical Substances HLA-DP beta-Chains ; HLA-DPw2 antigen ; Ions ; Beryllium (OW5102UV6N)
    Language English
    Publishing date 2019-12-04
    Publishing country England
    Document type Journal Article
    ZDB-ID 1476244-4
    ISSN 1463-9084 ; 1463-9076
    ISSN (online) 1463-9084
    ISSN 1463-9076
    DOI 10.1039/c9cp05695e
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Effect of Transition Metal Fragments on the Reverse Fritsch-Buttenberg-Wiechell Type Ring Contraction Reaction of Metallabenzynes to Metal-Carbene Complexes.

    Anusha, Chakkittakandiyil / De, Susmita / Parameswaran, Pattiyil

    The journal of physical chemistry. A

    2018  Volume 122, Issue 8, Page(s) 2160–2167

    Abstract: Metallabenzynes (1M), contrary to their organic analogues, benzynes, undergo ring-contraction to metal-carbene complexes (2M) via a reverse Fritsch-Buttenberg-Wiechell (FBW) type rearrangement. A detailed computational quantum mechanical study has been ... ...

    Abstract Metallabenzynes (1M), contrary to their organic analogues, benzynes, undergo ring-contraction to metal-carbene complexes (2M) via a reverse Fritsch-Buttenberg-Wiechell (FBW) type rearrangement. A detailed computational quantum mechanical study has been carried out to understand the effect of different third row transition metal fragments (ML
    Language English
    Publishing date 2018-03-01
    Publishing country United States
    Document type Journal Article
    ISSN 1520-5215
    ISSN (online) 1520-5215
    DOI 10.1021/acs.jpca.7b10335
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Different Donor-Acceptor Interactions of Carbene Ligands in Heteroleptic Divalent Group 14 Compounds, LEL' (E=C-Sn; L=N-Heterocyclic Carbene; L'=Cyclic Alkyl(Amino) Carbene).

    Purushothaman, Indu / De, Susmita / Parameswaran, Pattiyil

    Chemistry (Weinheim an der Bergstrasse, Germany)

    2018  Volume 24, Issue 15, Page(s) 3816–3824

    Abstract: The electronic structure and reactivity of heteroleptic divalent group 14 compounds, 1E (E=C-Sn) with NHC and cAAC ligands have been studied at the BP86/TZ2P level of theory and compared with homoleptic group 14 compounds. The EDA-NOCV (energy ... ...

    Abstract The electronic structure and reactivity of heteroleptic divalent group 14 compounds, 1E (E=C-Sn) with NHC and cAAC ligands have been studied at the BP86/TZ2P level of theory and compared with homoleptic group 14 compounds. The EDA-NOCV (energy decomposition analysis-natural orbitals for chemical valence) analysis indicates that the interaction between the two carbene ligands and the central C-atom in 1C can be best represented as one 3c-2e electron sharing σ-bond and one 3c-2e donor-acceptor σ-bond. There exists an electron sharing interaction between the π-type orbital on the central C-atom and the C-N π* orbital of cAAC and a π-back-donation from the σ-type lone pair on the central C-atom to the π*-MO of NHC. This bonding description is equivalent to the localized bonding representation, where the central C-atom forms two electron sharing bonds and two donor-acceptor bonds with cAAC and NHC ligands. However, the bonding between the carbene ligands and the heavier group 14 element can be best represented as two 2c-2e donor-acceptor σ-bonds and a π-back-donation from group 14 element to C-N π* orbital of cAAC. This bonding description is well supported by the geometrical and Natural Bond Orbital (NBO) analyses. Hence, 1C can be best described as a carbene and the heavier analogues can be best described as tetrylones. However, the high first (287.6-274.3 kcal mol
    Language English
    Publishing date 2018-03-12
    Publishing country Germany
    Document type Journal Article
    ZDB-ID 1478547-x
    ISSN 1521-3765 ; 0947-6539
    ISSN (online) 1521-3765
    ISSN 0947-6539
    DOI 10.1002/chem.201705719
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Ring contraction of metallabenzooxirene to metal carbonyl complexes - a comparative study with the Wolff rearrangement of oxirene and benzooxirene.

    Anusha, Chakkittakandiyil / De, Susmita / Parameswaran, Pattiyil

    Dalton transactions (Cambridge, England : 2003)

    2017  Volume 46, Issue 40, Page(s) 13974–13982

    Abstract: A detailed quantum mechanical study on the role of transition metal fragments towards the epoxidation reaction of metallabenzynes (1M, M = Fe, Ru, Os) to give metallabenzyne epoxide or metallabenzooxirene (2M), followed by the Wolff type 1,2- ... ...

    Abstract A detailed quantum mechanical study on the role of transition metal fragments towards the epoxidation reaction of metallabenzynes (1M, M = Fe, Ru, Os) to give metallabenzyne epoxide or metallabenzooxirene (2M), followed by the Wolff type 1,2-rearrangement to give metal carbonyls (4M), has been carried out at the M06/def2-TZVPP//BP86/def2-SVP level of theory. The epoxide or oxirene product (2A) of linear alkynes like acetylene is unstable and converts to a ketene (4A) by highly exothermic (-78.7 kcal mol
    Language English
    Publishing date 2017-10-17
    Publishing country England
    Document type Journal Article
    ZDB-ID 1472887-4
    ISSN 1477-9234 ; 1364-5447 ; 0300-9246 ; 1477-9226
    ISSN (online) 1477-9234 ; 1364-5447
    ISSN 0300-9246 ; 1477-9226
    DOI 10.1039/c7dt02911j
    Database MEDical Literature Analysis and Retrieval System OnLINE

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