Biology subjects

Kannan, D.

Publications and source records attributed to Kannan, D..

5 recordsLinked to original sources

bioRxiv2025

Mechanism for evolution of diverse autologous antibodies upon broadly neutralizing antibody therapy of people with HIV

Antiretroviral therapy (ART) inhibits Human Immunodeficiency Virus (HIV) replication to maintain undetectable viral loads in people living with HIV, but does not result in a cure. Due to the significant challenges of lifelong ART for many, there is strong interest in therapeutic strategies that result in cure. Recent clinical trials have shown that administration of broadly neutralizing antibodies (bnAbs) when there is some viremia can lead to ART-free viral control in some people; however, the underlying mechanisms are unclear. Our computational modeling shows that bnAbs administered in the presence of some viremia promote the evolution of autologous antibodies (aAbs) that target diverse epitopes of HIV spike proteins. This "net" of polyclonal aAbs could confer control since evasion of this response would require developing mutations in multiple epitopes. Our results provide a common mechanistic framework underlying recent clinical observations upon bnAb/ART therapy, and they should also motivate and inform new trials.

immunology↗

bioRxiv2024

RNA gradients can guide condensates toward promoters: implications for enhancer-promoter contacts and condensate-promoter kissing

We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein-RNA interactions. Our results indicate that condensates can show directed motion towards the promoter, driven by gradients in the RNA concentration. Analytical theory, consistent with simulations, predicts that the droplet velocity has a non-monotonic dependence on the distance to the promoter. We explore the consequences of this gradient-sensing mechanism for enhancer-promoter (E-P) communication using polymer simulations of the intervening chromatin chain. Directed motion of enhancer-bound condensates can, together with loop extrusion by cohesin, collaboratively increase the enhancer-promoter contact probability. Finally, we investigate under which conditions condensates can exhibit oscillations in their morphology and in the distance to the promoter. Oscillatory dynamics are caused by a delayed response of transcription to condensate-promoter contact and negative feedback from the accumulation of RNA at the promoter, which results in charge repulsion.

biophysics↗

bioRxiv2024

Essential role for HSP40 in asexual replication and thermotolerance of malaria parasites

Plasmodium falciparum, the parasite responsible for nearly all cases of severe malaria, must survive challenging environments to persist in its human host. Symptomatic malaria is characterized by periodic fevers corresponding to the 48-hour asexual reproduction of P. falciparum in red blood cells. As a result, P. falciparum has evolved a diverse collection of heat shock proteins to mitigate the stresses induced by temperature shifts. Among the assortment of heat shock proteins in P. falciparum, there is only one predicted canonical cytosolic J domain protein, HSP40 (PF3D7_1437900). Here, we generate a HSP40 tunable knockdown strain of P. falciparum to investigate the biological function of HSP40 during the intraerythrocytic lifecycle. We determine that HSP40 is required for malaria parasite asexual replication and survival of febrile temperatures. Previous reports have connected proteotoxic and thermal stress responses in malaria parasites. However, we find HSP40 has a specific role in heat shock survival and does not mitigate the proteotoxic stresses induced by artemisinin or proteosome inhibition. Following HSP40 knockdown, malaria parasites have a cell cycle progression defect and reduced nuclear replication. Untargeted proteomics reveal HSP40 depletion leads to a multifaceted downregulation of DNA replication and repair pathways. Additionally, we find HSP40 knockdown sensitizes parasites to DNA replication inhibition. Overall, these studies define the specialized role of the J domain protein HSP40 in malaria parasites during the blood stages of infection. Author SummaryMalaria parasites have evolved to survive and cause disease in humans even when they are challenged by the temperature shifts of fever. We are interested in uncovering how malaria parasites persist despite exposure to febrile temperatures. We know the parasite has a diverse collection of heat shock proteins that are important for proper folding of many proteins within cells during stress conditions. In this study, we define the role of one specific heat shock protein, HSP40, by generating a strain of the human malaria parasite P. falciparum where we control the expression of HSP40 during the red blood cell stages of infection. We find that HSP40 is required for malaria parasites to replicate in red blood cells. We demonstrate HSP40 expression to be vital for malaria parasite survival of febrile temperature stress. Additionally, we determine that without HSP40, DNA replication and repair is disrupted. Our work has uncovered essential parasite biology that may be exploited for the development of new antimalarials.

microbiology↗

bioRxiv2022

Polymer folding through active processes recreates features of genome organization

From proteins to chromosomes, polymers fold into specific conformations that control their biological function. Polymer folding has long been studied with equilibrium thermodynamics, yet intracellular organization and regulation involve energy-consuming, active processes. Signatures of activity have been measured in the context of chromatin motion, which shows spatial correlations and enhanced subdiffusion only in the presence of adenosine triphosphate (ATP). Moreover, chromatin motion varies with genomic coordinate, pointing towards a heterogeneous pattern of active processes along the sequence. How do such patterns of activity affect the conformation of a polymer such as chromatin? We address this question by combining analytical theory and simulations to study a polymer subjected to sequence-dependent correlated active forces. Our analysis shows that a local increase in activity (larger active forces) can cause the polymer backbone to bend and expand, while less active segments straighten out and condense. Our simulations further predict that modest activity differences can drive compartmentalization of the polymer consistent with the patterns observed in chromosome conformation capture experiments. Moreover, segments of the polymer that show correlated active (sub)diffusion attract each other through effective long-ranged harmonic interactions, whereas anticorrelations lead to effective repulsions. Thus, our theory offers non-equilibrium mechanisms for forming genomic compartments, which cannot be distinguished from affinity-based folding using structural data alone. As a first step toward disentangling active and passive mechanisms of folding, we discuss a data-driven approach to discern if and how active processes affect genome organization.

biophysics↗

bioRxiv2019

Heterogeneity in Nucleosome Spacing Governs Chromatin Elasticity

Within a living cell, the myriad of proteins that bind DNA introduce heterogeneously spaced kinks into an otherwise semiflexible DNA double helix. To investigate the effects of heterogeneous nucleosome binding on chromatin organization, we extend the wormlike chain (WLC) model to include statistically spaced, rigid kinks. On time scales where nucleosome positions are fixed, we find that the probability of chromatin loop formation can differ by up to six orders of magnitude between two sets of nucleosome positions drawn from the same distribution. On longer time scales, we show that continuous re-randomization due to nucleosome turnover results in chromatin tracing out an effective WLC with a dramatically smaller Kuhn length than bare DNA. Together, these observations demonstrate that heterogeneity in nucleosome spacing acts as the dominant source of chromatin elasticity and governs both local and global chromatin organization.

biophysics↗