Biology subjects

Hora, R.

Publications and source records attributed to Hora, R..

8 recordsLinked to original sources

bioRxiv2025

Plasmodium Repetome: A mysterious space with a wealth of information

Eukaryotic proteomes harbour repetitive stretches of amino acids that may play critical roles in the biology of that organism. While several tandem repeats (TR) are known to contribute to protein structure and function, information about the vast majority of repeat regions remains obscure. In this article, we have analysed the repeat content of different Plasmodium species and found the leading human malaria-causing P. falciparum (Pf) and P. vivax to be exceptionally rich in TR regions (>40% TR containing proteins). Detailed analysis of Pf repetome showed this intracellular parasite to carry longer TRs, several of which were present in exported proteins important for parasite survival and immune evasion. The repeat regions of Pf were enriched in acidic amino acids and asparagine (Asn), where Asn was more abundant in short and intermediate TRs, suggesting an evolutionary bias influenced by replication slippage and positive selection. Gene ontology analysis of TR containing Pf proteins helped us to understand their cellular localization along with the molecular and biological processes they are involved in. The Pf variable surface antigen families with roles in important pathogenic processes like cytoadherence, immune evasion etc. had low repeat content present within seroreactive peptides. Three-dimensional structure predictions of TR regions revealed several repeats to adopt ordered super-secondary conformations that are known to facilitate intermolecular interactions. Overall, this is a comprehensive study attempting to gain insights on the importance of TRs in malaria parasite biology and suggests a novel route to understanding protein function through the characterization of repeat content.

bioinformatics↗

bioRxiv2023

Exploring the interaction of inhibitor YM-1 with Plasmodium falciparum HSP70s through in silico methods

YM-1 belongs to the rhodacyanine class of the 70kDa heat shock protein (Hsp70) inhibitors. It antagonizes nucleotide exchange factor (NEF) BAG3 to block the critical ATPase cycle of HSP70 chaperones thereby disabling them. The anti-cancer potential of this small molecule derivative of MKT-077 is attributed to its improved solubility and stability over its parent. In the current study, we have used bioinformatics tools including molecular docking to study the binding strength of YM-1 for Plasmodium falciparum (Pf) HSP70s. Of the four PfHSP70 homologs, the mitochondrial counterpart was predicted to bind most efficiently with YM-1 at a previously reported inhibitor binding site. The interaction of YM-1 with mitochondrial PfHSP70 was significantly better than with any of the other Pf homologs. Further analysis of this PfHSP70-YM-1 complex helped us to predict not just the types of interactions, but also specific residues of the protein involved in inhibitor engagement. Information reported in this article is important from the standpoint of design and development of newer rhodacyanine based drugs against malaria.

bioinformatics↗

bioRxiv2023

Analyzing interaction of rhodacyanine inhibitor MKT-077 with Plasmodium falciparum HSP70 nucleotide binding domains

MKT-077 and its derivatives are rhodacyanine inhibitors that hold potential in treatment of cancer, neurodegenerative diseases and malaria. These allosteric drugs act by inhibiting the ATPase action of heat shock proteins of 70kDa (HSP70). MKT-077 accumulates in the mitochondria and displays differential activity against HSP70 homologs. The four Plasmodium falciparum HSP70s (PfHSP70) are present at various subcellular locations to perform distinct functions. In the present study, we have used bioinformatics tools to understand interactions between MKT-077 and PfHSP70s. Nature of the identified interactions is primarily hydrophobic with different PfHSP70 homologs showing variable propensity to bind MKT-077. Our molecular docking approach has helped us to predict the binding pocket and specific residues on PfHSP70s that are involved in interacting with MKT-077. Information derived from this article may form the foundation for design and development of MKT-077 based drugs against malaria.

bioinformatics↗

bioRxiv2023

Understanding the structural basis for differential binding of lapachol with PfHSP70s

The 70 kDa heat shock proteins from Plasmodium falciparum (PfHSP70) are an important family of proteins that may be exploited for antimalarial design. Plant derived inhibitor lapachol is reported to efficiently inhibit the exported PfHSP70-x while having poor activity against the parasite PfHSP70-1. In the present study, we have used in silico tools including molecular docking to understand the molecular basis for the above differences in lapachol inhibition activity against PfHSP70s. We found a significant gap in the binding energies and hence affinity of PfHSP70-1 and PfHSP70-x for lapachol with the latter having a better binding propensity. Our data highlight notable differences in the type of interactions between the two complexes. Detailed molecular analysis of the complexes has helped us to predict specific amino acid residues from both these PfHSP70 homologs that may be involved in lapachol binding. The above information may be utilized for design of PfHSP70 inhibitors with antimalarial potential.

bioinformatics↗

bioRxiv2023

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

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.

bioinformatics↗

bioRxiv2023

Understanding the molecular basis for enhanced glutenase activity of actinidin

Management of gluten intolerance is currently possible only by consumption of gluten free diet(GFD) for a lifetime. The scientific community has been searching for alternatives to GFD, like inclusion of natural proteases with meals or pre-treatment of gluten containing foods with glutenases. Actinidin from kiwifruit has shown considerable promise in digesting immunogenic gliadin peptides as compared to other plant derived cysteine proteases. Through this article, we have attempted to understand the structural basis for elevated protease action of actinidin against gliadin peptides by using an in silico approach. Docking experiments reveal key differences between the binding of gliadin peptide to actinidin and papain, which may be responsible for their differential digestive action. Sequence comparison of different plant cysteine proteases highlights amino acid residues surrounding the active site pocket of actinidin that are unique to this molecule and hence likely to contribute to its digestive properties. Graphical summary O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=64 SRC="FIGDIR/small/542047v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@4fcd61org.highwire.dtl.DTLVardef@134c371org.highwire.dtl.DTLVardef@10b5d78org.highwire.dtl.DTLVardef@1257d19_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

CX3CL1 binding protein-2 (CBP2) of Plasmodium falciparum binds nucleic acids

Several exported Plasmodium falciparum(Pf) proteins contribute to malaria biology through their involvement in cytoadherence, immune evasion and host cell remodelling. Many of these exported proteins and other host molecules are present in iRBC (infected red blood cell) generated extracellular vesicles (EVs), which are responsible for host cell modification and parasite development. CX3CL1 binding proteins (CBPs) present on the surface of iRBC have been reported to contribute to cytoadhesion by binding with the chemokine CX3CL1 via their extracellular domains. Here, we have characterized the cytoplasmic domain of CBP2to understand its function in parasite biology using biochemical and biophysical methods. Recombinant cytoplasmic CBP2 (rcCBP2) binds nucleic acids showing interaction with DNA/RNA. rcCBP2 shows dimer formation under non-reducing conditions highlighting the role of disulphide bonds in oligomerization while ATP binding leads to structural changes in the protein. In vitro interaction studies depict its binding with a Maurers cleft resident protein PfSBP1, which is influenced by ATP binding of rcCBP2. Our results suggest CBP2 as a two-transmembrane (2TM) receptor responsible for targeting EVs and delivering cargo to host endothelial cells. We propose CBP2 as an important molecule having roles in cytoadherence and immune modulation through its extracellular and cytoplasmic domains respectively.

molecular biology↗

bioRxiv2018

Cholesterol bound Plasmodium falciparum co-chaperone ‘PFA0660w’ complexes with major virulence factor ‘PfEMP1’ via chaperone ‘PfHsp70-x’

Lethality of Plasmodium falciparum (Pf) caused malaria results from cytoadherence, which is effected by exported Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1) family. Several exported Pf proteins (exportome) including chaperones alongside cholesterol rich microdomains are crucial for PfEMP1 translocation to infected erythrocyte surface. An exported Hsp40 (heat shock protein 40) PFA0660w functions as a co-chaperone of PfHsp70-x, and these co-localize to specialized intracellular mobile structures termed J-dots. Our studies attempt to understand the function of PFA0660w-PfHsp70-x chaperone pair using recombinant proteins. Biochemical assays reveal that N and C-terminal domains of PFA0660w and PfHsp70-x respectively are critical for their activity. We show the novel direct interaction of PfHsp70-x with the cytoplasmic tail of PfEMP1, and binding of PFA0660w with cholesterol. PFA0660w operates both as a chaperone and lipid binding molecule via its separate substrate and cholesterol binding sites. PfHsp70-x binds cholesterol linked PFA0660w and PfEMP1 simultaneously in vitro to form a complex. Collectively, our results and the past literature support the hypothesis that PFA0660w-PfHsp70-x chaperone pair assists PfEMP1 transport across the host erythrocyte through cholesterol containing J-dots. Since PFA0660w seems essential for parasite survival, characterization of its interaction with PfHsp70-x and J-dots may form the basis for development of future antimalarials.

molecular biology↗