LIVIVO - Search results -

Search results

Result 1 - 10 of total 18

Search options

Article ; Online: Enhancement of SARS-CoV-2 Infection via Crosslinking of Adjacent Spike Proteins by N-Terminal Domain-Targeting Antibodies.

Lusiany, Tina / Terada, Tohru / Kishikawa, Jun-Ichi / Hirose, Mika / Chen, David Virya / Sugihara, Fuminori / Ismanto, Hendra Saputra / van Eerden, Floris J / Li, Songling / Kato, Takayuki / Arase, Hisashi / Yoshiharu, Matsuura / Okada, Masato / Standley, Daron M

Viruses

2023 Volume 15, Issue 12

Abstract: The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant ... ...

Abstract	The entry of SARS-CoV-2 into host cells is mediated by the interaction between the spike receptor-binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2). Certain human antibodies, which target the spike N-terminal domain (NTD) at a distant epitope from the host cell binding surface, have been found to augment ACE2 binding and enhance SARS-CoV-2 infection. Notably, these antibodies exert their effect independently of the antibody fragment crystallizable (Fc) region, distinguishing their mode of action from previously described antibody-dependent infection-enhancing (ADE) mechanisms. Building upon previous hypotheses and experimental evidence, we propose that these NTD-targeting infection-enhancing antibodies (NIEAs) achieve their effect through the crosslinking of neighboring spike proteins. In this study, we present refined structural models of NIEA fragment antigen-binding region (Fab)-NTD complexes, supported by molecular dynamics simulations and hydrogen-deuterium exchange mass spectrometry (HDX-MS). Furthermore, we provide direct evidence confirming the crosslinking of spike NTDs by NIEAs. Collectively, our findings advance our understanding of the molecular mechanisms underlying NIEAs and their impact on SARS-CoV-2 infection.
MeSH term(s)	Humans ; COVID-19 ; SARS-CoV-2 ; Angiotensin-Converting Enzyme 2/metabolism ; Spike Glycoprotein, Coronavirus ; Protein Binding ; Antibodies, Viral
Chemical Substances	Angiotensin-Converting Enzyme 2 (EC 3.4.17.23) ; spike protein, SARS-CoV-2 ; Spike Glycoprotein, Coronavirus ; Antibodies, Viral
Language	English
Publishing date	2023-12-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2516098-9
ISSN	1999-4915 ; 1999-4915
ISSN (online)	1999-4915
ISSN	1999-4915
DOI	10.3390/v15122421
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

This service is chargeable due to the Delivery terms set by subito. Orders including an article and supplementary material will be classified as separate orders. In these cases, fees will be demanded for each order.

Article ; Online: Structural Modeling of Lymphocyte Receptors and Their Antigens.

Li, Songling / Wilamowski, Jan / Teraguchi, Shunsuke / van Eerden, Floris J / Rozewicki, John / Davila, Ana / Xu, Zichang / Katoh, Kazutaka / Standley, Daron M

Methods in molecular biology (Clifton, N.J.)

2019 Volume 2048, Page(s) 207–229

Abstract: Structural modeling plays a key role in protein function prediction on a genome-wide scale. For B and T lymphocyte receptors, the critical functional question is: which antigens and epitopes are targeted? With emerging B cell receptor (BCR) and T cell ... ...

Abstract	Structural modeling plays a key role in protein function prediction on a genome-wide scale. For B and T lymphocyte receptors, the critical functional question is: which antigens and epitopes are targeted? With emerging B cell receptor (BCR) and T cell receptor (TCR) sequencing methods improving in both breadth and depth, there is a growing need for methods that can help answer this question. Since lymphocyte-antigen recognition depends on complementarity, structural modeling is likely to play an important role in understanding antigen specificity and affinity. In the case of BCRs, such modeling methods have a long history in the study and design of antibodies. However, for TCRs there are relatively few publicly available modeling tools, and, to our knowledge, none that incorporate interaction between TCRs and peptide-MHC (pMHC) complexes. Here, we provide a web-based tool, ImmuneScape ( https://sysimm.org/immune-scape/ ), to carry out TCR-pMHC modeling as a first step toward structure-based function prediction.
MeSH term(s)	Alleles ; Epitope Mapping/methods ; Epitopes, T-Lymphocyte/genetics ; Epitopes, T-Lymphocyte/immunology ; Epitopes, T-Lymphocyte/metabolism ; HLA Antigens/genetics ; HLA Antigens/immunology ; HLA Antigens/metabolism ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Receptors, Antigen, T-Cell/genetics ; Receptors, Antigen, T-Cell/immunology ; Receptors, Antigen, T-Cell/metabolism ; Sequence Alignment ; Software ; Structure-Activity Relationship ; T-Lymphocytes/immunology ; T-Lymphocytes/metabolism
Chemical Substances	Epitopes, T-Lymphocyte ; HLA Antigens ; Receptors, Antigen, T-Cell
Language	English
Publishing date	2019-08-08
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-9728-2_17
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Details ▾
- Full text online
- Order with fees

Article ; Online: Exchange pathways of plastoquinone and plastoquinol in the photosystem II complex.

Van Eerden, Floris J / Melo, Manuel N / Frederix, Pim W J M / Periole, Xavier / Marrink, Siewert J

Nature communications

2017 Volume 8, Page(s) 15214

Abstract: Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome ... ...

Abstract	Plastoquinone (PLQ) acts as an electron carrier between photosystem II (PSII) and the cytochrome b
MeSH term(s)	Diffusion ; Electron Transport ; Models, Biological ; Molecular Dynamics Simulation ; Oxidation-Reduction ; Photosynthesis ; Photosystem II Protein Complex/metabolism ; Plant Leaves/metabolism ; Plastoquinone/analogs & derivatives ; Plastoquinone/metabolism ; Thylakoids/metabolism ; Time Factors
Chemical Substances	Photosystem II Protein Complex ; plastoquinol (3819-09-8) ; Plastoquinone (OAC30J69CN)
Language	English
Publishing date	2017-05-10
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2041-1723
ISSN (online)	2041-1723
DOI	10.1038/ncomms15214
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Celastrol suppresses humoral immune responses and autoimmunity by targeting the COMMD3/8 complex.

Science immunology

2023 Volume 8, Issue 81, Page(s) eadc9324

Abstract: Celastrol, a bioactive molecule extracted from ... ...

Abstract	Celastrol, a bioactive molecule extracted from the
MeSH term(s)	Mice ; Animals ; Immunity, Humoral ; Autoimmunity ; Pentacyclic Triterpenes ; Autoimmune Diseases
Chemical Substances	celastrol (L8GG98663L) ; Pentacyclic Triterpenes
Language	English
Publishing date	2023-03-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	2470-9468
ISSN (online)	2470-9468
DOI	10.1126/sciimmunol.adc9324
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article ; Online: Prediction of Thylakoid Lipid Binding Sites on Photosystem II.

Van Eerden, Floris J / Melo, Manuel N / Frederix, Pim W J M / Marrink, Siewert J

Biophysical journal

2017 Volume 113, Issue 12, Page(s) 2669–2681

Abstract: The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To ...

Abstract	The thylakoid membrane has a unique lipid composition, consisting mostly of galactolipids. These thylakoid lipids have important roles in photosynthesis. Here, we investigate to what extent these lipids bind specifically to the Photosystem II complex. To this end, we performed coarse-grain MD simulations of the Photosystem II complex embedded in a thylakoid membrane with realistic composition. Based on >85 μs simulation time, we find that monogalactosyldiacylglycerol and sulfoquinovosyldiacylglycerol lipids are enriched in the annular shell around the protein, and form distinct binding sites. From the analysis of residue contacts, we conclude that electrostatic interactions play an important role in stabilizing these binding sites. Furthermore, we find that chlorophyll a has a prevalent role in the coordination of the lipids. In addition, we observe lipids to diffuse in and out of the plastoquinone exchange cavities, allowing exchange of cocrystallized lipids with the bulk membrane and suggesting a more open nature of the plastoquinone exchange cavity. Together, our data provide a wealth of information on protein-lipid interactions for a key protein in photosynthesis.
MeSH term(s)	Binding Sites ; Glycerol/metabolism ; Membrane Lipids/metabolism ; Molecular Dynamics Simulation ; Photosystem II Protein Complex/chemistry ; Photosystem II Protein Complex/metabolism ; Protein Binding ; Protein Conformation ; Thylakoids/metabolism
Chemical Substances	Membrane Lipids ; Photosystem II Protein Complex ; Glycerol (PDC6A3C0OX)
Language	English
Publishing date	2017-12-19
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.09.039
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 2: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article: Flexible, Functional, and Familiar: Characteristics of SARS-CoV-2 Spike Protein Evolution.

Saputri, Dianita S / Li, Songling / van Eerden, Floris J / Rozewicki, John / Xu, Zichang / Ismanto, Hendra S / Davila, Ana / Teraguchi, Shunsuke / Katoh, Kazutaka / Standley, Daron M

Frontiers in microbiology

2020 Volume 11, Page(s) 2112

Abstract: The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection ... ...

Abstract	The SARS-CoV-2 S protein is a major point of interaction between the virus and the human immune system. As a consequence, the S protein is not a static target but undergoes rapid molecular evolution. In order to more fully understand the selection pressure during evolution, we examined residue positions in the S protein that vary greatly across closely related viruses but are conserved in the subset of viruses that infect humans. These "evolutionarily important" residues were not distributed evenly across the S protein but were concentrated in two domains: the N-terminal domain and the receptor-binding domain, both of which play a role in host cell binding in a number of related viruses. In addition to being localized in these two domains, evolutionary importance correlated with structural flexibility and inversely correlated with distance from known or predicted host receptor-binding residues. Finally, we observed a bias in the composition of the amino acids that make up such residues toward more human-like, rather than virus-like, sequence motifs.
Keywords	covid19
Language	English
Publishing date	2020-09-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2587354-4
ISSN	1664-302X
ISSN	1664-302X
DOI	10.3389/fmicb.2020.02112
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Article ; Online: Design and Properties of Genetically Encoded Probes for Sensing Macromolecular Crowding.

Liu, Boqun / Åberg, Christoffer / van Eerden, Floris J / Marrink, Siewert J / Poolman, Bert / Boersma, Arnold J

Biophysical journal

2017 Volume 112, Issue 9, Page(s) 1929–1939

Abstract: Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of ... ...

Abstract	Cells are highly crowded with proteins and polynucleotides. Any reaction that depends on the available volume can be affected by macromolecular crowding, but the effects of crowding in cells are complex and difficult to track. Here, we present a set of Förster resonance energy transfer (FRET)-based crowding-sensitive probes and investigate the role of the linker design. We investigate the sensors in vitro and in vivo and by molecular dynamics simulations. We find that in vitro all the probes can be compressed by crowding, with a magnitude that increases with the probe size, the crowder concentration, and the crowder size. We capture the role of the linker in a heuristic scaling model, and we find that compression is a function of size of the probe and volume fraction of the crowder. The FRET changes observed in Escherichia coli are more complicated, where FRET-increases and scaling behavior are observed solely with probes that contain the helices in the linker. The probe with the highest sensitivity to crowding in vivo yields the same macromolecular volume fractions as previously obtained from cell dry weight. The collection of new probes provides more detailed readouts on the macromolecular crowding than a single sensor.
MeSH term(s)	Escherichia coli/metabolism ; Fluorescence Resonance Energy Transfer ; Fluorometry ; Macromolecular Substances/metabolism ; Microscopy, Confocal ; Microscopy, Fluorescence ; Molecular Dynamics Simulation ; Molecular Imaging ; Molecular Probes/chemistry ; Molecular Probes/genetics
Chemical Substances	Macromolecular Substances ; Molecular Probes
Language	English
Publishing date	2017-05-09
Publishing country	United States
Document type	Journal Article
ZDB-ID	218078-9
ISSN	1542-0086 ; 0006-3495
ISSN (online)	1542-0086
ISSN	0006-3495
DOI	10.1016/j.bpj.2017.04.004
Database	MEDical Literature Analysis and Retrieval System OnLINE

In stock of ZB MED Cologne/Königswinter

Zs.A 235: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MO 2: Show issues

Order via subito

Details ▾
- See ZB MED holdings
- Order with fees

Article ; Online: Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane.

van Eerden, Floris J / van den Berg, Tom / Frederix, Pim W J M / de Jong, Djurre H / Periole, Xavier / Marrink, Siewert J

The journal of physical chemistry. B

2017 Volume 121, Issue 15, Page(s) 3237–3249

Abstract: Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 μs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid ... ...

Abstract	Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 μs molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible toward the periphery of the complex as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, β-carotenes show the highest mobility. Some of the β-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast with the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.
Language	English
Publishing date	2017-04-20
Publishing country	United States
Document type	Journal Article
ISSN	1520-5207
ISSN (online)	1520-5207
DOI	10.1021/acs.jpcb.6b06865
Database	MEDical Literature Analysis and Retrieval System OnLINE

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane

van Eerden, Floris J / van den Berg Tom / Frederix Pim W. J. M / de Jong Djurre H / Periole Xavier / Marrink Siewert J

Journal of physical chemistry. 2017 Apr. 20, v. 121, no. 15

2017

Abstract: Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 Î¼s molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid ...

Abstract	Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 Î¼s molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup of the protein complex and the many natural cofactors and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible toward the periphery of the complex as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, Î²-carotenes show the highest mobility. Some of the Î²-carotenes diffuse in and out of the protein complex via the thylakoid membrane. In contrast with the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.
Keywords	energy transfer ; glycolipids ; lipid composition ; models ; molecular dynamics ; photosystem II ; protein subunits ; thylakoids
Language	English
Dates of publication	2017-0420
Size	p. 3237-3249.
Publishing place	American Chemical Society
Document type	Article
ISSN	1520-5207
DOI	10.1021%2Facs.jpcb.6b06865
Database	NAL-Catalogue (AGRICOLA)

Order via subito

Inter-library loan at ZB MED

Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

Article: Methods for sequence and structural analysis of B and T cell receptor repertoires.

Teraguchi, Shunsuke / Saputri, Dianita S / Llamas-Covarrubias, Mara Anais / Davila, Ana / Diez, Diego / Nazlica, Sedat Aybars / Rozewicki, John / Ismanto, Hendra S / Wilamowski, Jan / Xie, Jiaqi / Xu, Zichang / Loza-Lopez, Martin de Jesus / van Eerden, Floris J / Li, Songling / Standley, Daron M

Computational and structural biotechnology journal

2020 Volume 18, Page(s) 2000–2011

Abstract: B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of ... ...

Abstract	B cell receptors (BCRs) and T cell receptors (TCRs) make up an essential network of defense molecules that, collectively, can distinguish self from non-self and facilitate destruction of antigen-bearing cells such as pathogens or tumors. The analysis of BCR and TCR repertoires plays an important role in both basic immunology as well as in biotechnology. Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data. Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features. After describing the recent sequencing technologies for immune receptor repertoires, we survey structural modeling methods for BCR and TCRs, along with methods for clustering such models. We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.
Keywords	covid19
Language	English
Publishing date	2020-07-17
Publishing country	Netherlands
Document type	Journal Article ; Review
ZDB-ID	2694435-2
ISSN	2001-0370
ISSN	2001-0370
DOI	10.1016/j.csbj.2020.07.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

Full text online

Accessible to users with ZB MED library card

Order via subito

Details ▾
- Full text online
- Order with fees

To top

More links

Kategorien

Order via subito

Full text online

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

More links

Kategorien

In stock of ZB MED Cologne/Königswinter

Order via subito

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

More links

Kategorien

Order via subito

Inter-library loan at ZB MED

Full text online

More links

Kategorien

Order via subito