Student or educator? Sign up with your school email and get 6 months of Pro free.
CoChat
Sign Up
PreprintCited by 0Malaria Research and ControlComputational Drug Discovery MethodsProtein Structure and Dynamics

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Investigating the ATP binding pocket of CX3CL1 binding protein 2 using in silico approach

Open access
Kumari, Rimjhim, Kaur, Satinder, Hora, Rachna, Mishra, Prakash Chandra·2023·Journal of Proteins and Proteomics
DOI 10.21203/rs.3.rs-2985578/v1

Preprint — published as 10.1007/s42485-024-00133-z · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Plasmodium falciparum (Pf) causes the most fatal form of malaria owing to its ability to cytoadhere in the microvasculature of various organs in the body. In addition to the Pf erythrocyte membrane protein 1 (PfEMP1) family that binds diverse host receptors, CX3CL1 binding proteins 1 and 2 (CBP1 and 2) also bind the endothelial chemokine ‘CX3CL1’ to effect cytoadhesion of parasite infected erthrocytes. CBP2 is a multifaceted protein that binds nucleic acids, Pf skeleton binding protein (PfSBP1) and ATP. ATP binding to the cytoplasmic domain of CBP2 (cCBP2) induces structural changes in the protein, and hints at its role in cell signaling. In this study, we have attempted to identify the ATP binding pocket of CBP2 using an in silico approach. We have also delineated the type of interactions and amino acid residues that are likely to bind ATP. As CX3CL1 binding proteins are central to parasite biology, the obtained information is likely to form the basis for inhibitor and drug design against this molecule.

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.21203/rs.3.rs-2985578/v1

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Show all 1 references

Research works printed but not linked: 34

  1. A. F. Cowman, J. Healer, D. Marapana, and K. Marsh, “Malaria: Biology and Disease,” Cell, vol. 167, no. 3, pp. 610–624, Oct. 2016, doi: 10.1016/j.cell.2016.07.055. · DOI
  2. N. J. White, “Malaria parasite clearance,” Malar. J., vol. 16, no. 1, p. 88, Feb. 2017, doi: 10.1186/s12936-017-1731-1. · DOI · Paper page
  3. M. Marti, R. T. Good, M. Rug, E. Knuepfer, and A. F. Cowman, “Targeting malaria virulence and remodeling proteins to the host erythrocyte,” Science, vol. 306, no. 5703, pp. 1930–1933, Dec. 2004, doi: 10.1126/science.1102452. · DOI
  4. N. Mohandas and X. An, “Malaria and human red blood cells,” Med. Microbiol. Immunol. (Berl.), vol. 201, no. 4, pp. 593–598, Nov. 2012, doi: 10.1007/s00430-012-0272-z. · DOI
  5. R. Hora, P. Kapoor, K. K. Thind, and P. C. Mishra, “Cerebral malaria – clinical manifestations and pathogenesis,” Metab. Brain Dis., vol. 31, no. 2, pp. 225–237, Apr. 2016, doi: 10.1007/s11011-015-9787-5. · DOI
  6. J. A. Rowe, A. Claessens, R. A. Corrigan, and M. Arman, “Adhesion of Plasmodium falciparum-infected erythrocytes to human cells: molecular mechanisms and therapeutic implications,” Expert Rev. Mol. Med., vol. 11, p. e16, May 2009, doi: 10.1017/S1462399409001082. · DOI
  7. T. Hatabu, S. I. Kawazu, M. Aikawa, and S. Kano, “Binding of Plasmodium falciparum-infected erythrocytes to the membrane-bound form of Fractalkine/CX3CL1,” Proc. Natl. Acad. Sci. U. S. A., vol. 100, no. 26, pp. 15942–15946, Dec. 2003, doi: 10.1073/pnas.2534560100. · DOI
  8. J. F. Bazan et al., “A new class of membrane-bound chemokine with a CX3C motif,” Nature, vol. 385, no. 6617, pp. 640–644, Feb. 1997, doi: 10.1038/385640a0. · DOI · Paper page
  9. O. Yoshie, T. Imai, and H. Nomiyama, “Chemokines in Immunity,” in Advances in Immunology, F. J. Dixon, Ed., Academic Press, 2001, pp. 57–110. doi: 10.1016/S0065-2776(01)78002-9. · DOI
  10. A. M. Fong et al., “Fractalkine and CX3CR1 mediate a novel mechanism of leukocyte capture, firm adhesion, and activation under physiologic flow,” J. Exp. Med., vol. 188, no. 8, pp. 1413–1419, Oct. 1998, doi: 10.1084/jem.188.8.1413. · DOI
  11. B. A. Jones, M. Beamer, and S. Ahmed, “Fractalkine/CX3CL1: A Potential New Target for Inflammatory Diseases,” Mol. Interv., vol. 10, no. 5, pp. 263–270, Oct. 2010, doi: 10.1124/mi.10.5.3. · DOI
  12. T. J. Sargeant et al., “Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites,” Genome Biol., vol. 7, no. 2, p. R12, 2006, doi: 10.1186/gb-2006-7-2-r12. · DOI
  13. P. Hermand, L. Cicéron, C. Pionneau, C. Vaquero, C. Combadière, and P. Deterre, “Plasmodium falciparum proteins involved in cytoadherence of infected erythrocytes to chemokine CX3CL1,” Sci. Rep., vol. 6, no. 1, Art. no. 1, Sep. 2016, doi: 10.1038/srep33786. · DOI
  14. M. J. Hossain et al., “Plasmodium falciparum Tudor Staphylococcal Nuclease interacting proteins suggest its role in nuclear as well as splicing processes,” Gene, vol. 468, no. 1–2, pp. 48–57, Nov. 2010, doi: 10.1016/j.gene.2010.08.004. · DOI
  15. B. E. Sleebs et al., “Inhibition of Plasmepsin V activity demonstrates its essential role in protein export, PfEMP1 display, and survival of malaria parasites,” PLoS Biol., vol. 12, no. 7, p. e1001897, Jul. 2014, doi: 10.1371/journal.pbio.1001897. · DOI
  16. A. Mbengue et al., “New Export Pathway in Plasmodium falciparum-Infected Erythrocytes: Role of the Parasite Group II Chaperonin, PfTRiC,” Traffic, vol. 16, no. 5, pp. 461–475, 2015, doi: 10.1111/tra.12266. · DOI
  17. P. J. McMillan et al., “Spatial and temporal mapping of the PfEMP1 export pathway in Plasmodium falciparum,” Cell. Microbiol., vol. 15, no. 8, pp. 1401–1418, Aug. 2013, doi: 10.1111/cmi.12125. · DOI
  18. T. Y. Sam-Yellowe, “The role of the Maurer’s clefts in protein transport in Plasmodium falciparum,” Trends Parasitol., vol. 25, no. 6, pp. 277–284, Jun. 2009, doi: 10.1016/j.pt.2009.03.009. · DOI
  19. R. Saxena, J. Kaur, R. Hora, P. Singh, V. Singh, and P. C. Mishra, “CX3CL1 binding protein-2 (CBP2) of Plasmodium falciparum binds nucleic acids,” Int. J. Biol. Macromol., vol. 138, pp. 996–1005, Oct. 2019, doi: 10.1016/j.ijbiomac.2019.07.178. · DOI
  20. P.-Y. Mantel et al., “Malaria-Infected Erythrocyte-Derived Microvesicles Mediate Cellular Communication within the Parasite Population and with the Host Immune System,” Cell Host Microbe, vol. 13, no. 5, pp. 521–534, May 2013, doi: 10.1016/j.chom.2013.04.009. · DOI · Paper page
  21. “Proteomic analysis of extracellular vesicles from a Plasmodium falciparum Kenyan clinical isolate defines a core parasite secretome - PMC.” https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5583745/ (accessed May 09, 2023).
  22. “Microvesicles from malaria-infected red blood cells activate natural killer cells via MDA5 pathway | PLOS Pathogens.” https://journals.plos.org/plospathogens/article?id=10.1371/journal.ppat.1007298 (accessed May 09, 2023). · DOI
  23. S. L. N. Maas, X. O. Breakefield, and A. M. Weaver, “Extracellular Vesicles: Unique Intercellular Delivery Vehicles,” Trends Cell Biol., vol. 27, no. 3, pp. 172–188, Mar. 2017, doi: 10.1016/j.tcb.2016.11.003. · DOI
  24. “Cell-Cell Communication between Malaria-Infected Red Blood Cells via Exosome-like Vesicles - ScienceDirect.” https://www.sciencedirect.com/science/article/pii/S0092867413005047 (accessed May 09, 2023).
  25. A. Maxwell and D. M. Lawson, “The ATP-Binding Site of Type II Topoisomerases as a Target for Antibacterial Drugs,” Curr. Top. Med. Chem., vol. 3, no. 3, pp. 283–303, Jan. 2003, doi: 10.2174/1568026033452500. · DOI
  26. J. S. Chauhan, N. K. Mishra, and G. P. Raghava, “Identification of ATP binding residues of a protein from its primary sequence,” BMC Bioinformatics, vol. 10, no. 1, p. 434, Dec. 2009, doi: 10.1186/1471-2105-10-434. · DOI
  27. J. Hu, Y. Li, Y. Zhang, and D.-J. Yu, “ATPbind: Accurate Protein–ATP Binding Site Prediction by Combining Sequence-Profiling and Structure-Based Comparisons,” J. Chem. Inf. Model., vol. 58, no. 2, pp. 501–510, Feb. 2018, doi: 10.1021/acs.jcim.7b00397. · DOI
  28. “UCSF Chimera—A visualization system for exploratory research and analysis - Pettersen – 2004 - Journal of Computational Chemistry - Wiley Online Library.” https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.20084 (accessed May 09, 2023). · DOI · Paper page
  29. J. Eberhardt, D. Santos-Martins, A. F. Tillack, and S. Forli, “AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings,” J. Chem. Inf. Model., vol. 61, no. 8, pp. 3891–3898, Aug. 2021, doi: 10.1021/acs.jcim.1c00203. · DOI
  30. R. A. Laskowski and M. B. Swindells, “LigPlot+: Multiple Ligand–Protein Interaction Diagrams for Drug Discovery,” J. Chem. Inf. Model., vol. 51, no. 10, pp. 2778–2786, Oct. 2011, doi: 10.1021/ci200227u. · DOI
  31. A. G. Maier et al., “Exported Proteins Required for Virulence and Rigidity of Plasmodium falciparum-Infected Human Erythrocytes,” Cell, vol. 134, no. 1, pp. 48–61, Jul. 2008, doi: 10.1016/j.cell.2008.04.051. · DOI
  32. M. Zhang et al., “Uncovering the essential genes of the human malaria parasite Plasmodium falciparum by saturation mutagenesis,” Science, vol. 360, no. 6388, p. eaap7847, May 2018, doi: 10.1126/science.aap7847. · DOI
  33. R. A. Laskowski, M. W. MacArthur, D. S. Moss, and J. M. Thornton, “PROCHECK: a program to check the stereochemical quality of protein structures,” J. Appl. Crystallogr., vol. 26, no. 2, Art. no. 2, Apr. 1993, doi: 10.1107/S0021889892009944. · DOI · Paper page
  34. “Frontiers | Structural Biology in the Clouds: The WeNMR-EOSC Ecosystem.” https://www.frontiersin.org/articles/10.3389/fmolb.2021.729513/full (accessed May 09, 2023). · DOI

Metadata

Authors
Kumari, R., Kaur, S., Hora, R., & Mishra, P. C.
Affiliations
Guru Nanak Dev University (IN)
Corresponding author
Mishra, Prakash Chandra
ORCID
Venue
Journal of Proteins and Proteomics
Publisher
Research Square Platform LLC
Published
2023-08-25
Volume
15
Issue
2
Pages
209-214
ISSN
0975-8151 (ISSN-L)
DOI
10.21203/rs.3.rs-2985578/v1
OpenAlex
W4393181328
Cited by
0
References
1
FWCI
0.00
Type
journal article
Language
en
Open access
Licence
Locations
  • Journal of Proteins and Proteomics (publishedVersion)
  • Research Square (acceptedVersion, cc-by)
Funders
  • Department of Biotechnology, Ministry of Science and Technology, India
  • Department of Science and Technology, Ministry of Science and Technology, India
Topics
  • Health Sciences › Medicine › Public Health, Environmental and Occupational Health › Malaria Research and Control
  • Life Sciences › Pharmacology, Toxicology and Pharmaceutics › Drug Discovery › Computational Drug Discovery Methods
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords
ATP binding site, Plasmodium falciparum, cytoadhesion, PfEMP1, fractalkine, chemokine binding, ATP binding, protein structure, therapeutic target, inhibitor design

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

How to cite

Cite CoChat for the checks on this page, and the paper for its own findings.

This page
CoChat. (2026). Citation check: Investigating the ATP binding pocket of CX3CL1 binding protein 2 using in silico approach. https://app.cochat.ai/papers/10.21203/rs.3.rs-2985578/v1
The paper
Kumari, R., Kaur, S., Hora, R., & Mishra, P. C. (2023). Investigating the ATP binding pocket of CX3CL1 binding protein 2 using in silico approach. Journal of Proteins and Proteomics. https://doi.org/10.21203/rs.3.rs-2985578/v1

Data sources

Bibliographic data: Semantic Scholar, OpenAlex, Crossref.

Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).

Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.