The Experts below are selected from a list of 77994 Experts worldwide ranked by ideXlab platform

Rudolf Podgornik - One of the best experts on this subject based on the ideXlab platform.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    Computational and structural biotechnology journal, 2021
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    ChemRxiv, 2020
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

W Y Ching - One of the best experts on this subject based on the ideXlab platform.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    Computational and structural biotechnology journal, 2021
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    ChemRxiv, 2020
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

Jose A Pomposo - One of the best experts on this subject based on the ideXlab platform.

  • effect of Molecular crowding on conformation and interactions of single chain nanoparticles
    Macromolecules, 2019
    Co-Authors: Julian Oberdisse, Marina Gonzalezburgos, Aranzazu Mendia, A Arbe, Angel J Moreno, Jose A Pomposo
    Abstract:

    Single-chain nanoparticles (SCNPs) are soft disordered nano-objects synthesized by intra-Molecular Bonding of linear polymer chains with a finite fraction of reactive groups allowing internal crosslinking of the molecule. They may be investigated as a mimick of, e.g., intrinsically disordered proteins, in particular with respect to the effect of the crowded cellular environment on macroMolecular properties. Here the conformation of synthetic SCNPs in presence of linear polystyrene crowding molecules has been studied by small-angle neutron scattering under contrast-matching of the crowders[1]. A model describing the scattering of aggregating polydisperse SCNPs (see Figure 1) has been developed, resulting in the determination of the potentially squeezed size of the individual SCNPs within aggregates, their local chain statistics, and the average aggregation number, as a function of crowding. Two different crowders – of low and high Molecular weight, respectively – are shown to have a different effect: while long chains tend to impede their aggregation above their overlap concentration, short ones are found to mediate depletion interactions leading to aggregation. Self-imposed crowding within the aggregates has a similar impact on chain conformation independently of the crowding of the surrounding medium. Our results are compared to recent simulations and is hoped to contribute to the microscopic understanding of the phase behavior of soft intrinsically disordered nano-objects, and in particular the effect of crowding on biomacromolecules. Figure 1: Schematic representation of the aggregation process of two SCNPs of monomer numbers i1 and i2 described by the addition of their individual SCNP masses, and obeying the same local chain statistics. References [1] Julian Oberdisse, Marina Gonzalez-Burgos, Ander Mendia, Arantxa Arbe, Angel J. Moreno, Jose A. Pomposo, Aurel Radulescu and Juan Colmenero, under (favorable) revision in Macromolecules.

Bahaa Jawad - One of the best experts on this subject based on the ideXlab platform.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    Computational and structural biotechnology journal, 2021
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    ChemRxiv, 2020
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

Puja Adhikari - One of the best experts on this subject based on the ideXlab platform.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    Computational and structural biotechnology journal, 2021
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. In the interaction among structural domains, we present new insights for crucial hinge-like movement and fusion process. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.

  • ultra large scale ab initio quantum chemical computation of bio Molecular systems the case of spike protein of sars cov 2 virus
    ChemRxiv, 2020
    Co-Authors: W Y Ching, Puja Adhikari, Bahaa Jawad, Rudolf Podgornik
    Abstract:

    The COVID-19 pandemic poses a severe threat to human health with an unprecedented social and economic disruption. Spike (S) glycoprotein of the SARS-CoV-2 virus is pivotal in understanding the virus anatomy, since it initiates the first contact with the ACE2 receptor in the human cell. We report results of ab initio computation of the spike protein, the largest ab initio quantum chemical computation to date on any bio-Molecular system, using a divide and conquer strategy by focusing on individual structural domains. In this approach we divided the S-protein into seven structural domains: N-terminal domain (NTD), receptor binding domain (RBD), subdomain 1 (SD1), subdomain 2 (SD2), fusion peptide (FP), heptad repeat 1 with central helix (HR1-CH) and connector domain (CD). The entire Chain A has 14,488 atoms including the hydrogen atoms but excluding the amino acids with missing coordinates based on the PDB data (ID: 6VSB). The results include structural refinement, ab initio calculation of intra-Molecular Bonding mechanism, 3- dimensional non-local inter-amino acid interaction with implications for the inter-domain interaction. Details of the electronic structure, interatomic Bonding, partial charge distribution and the role played by hydrogen bond network are discussed. Extension of such calculation to the interface between the S-protein binding domain and ACE2 receptor can provide a pathway for computational understanding of mutations and the design of therapeutic drugs to combat the COVID-19 pandemic.