| dc.description.abstract | In the scope of my thesis work, a concerted effort was undertaken to elucidate bi-
ological functions through the lens of structural analysis, employing protein dy-
namics. The role of protein dynamics in shaping and facilitating protein function,
by enabling exploration of the conformational landscape, was the primary objec-
tive. Proteins seldom function in isolation and they often engage in complexes with
other macromolecules such as other proteins, DNA, RNA, and small molecules.
In this chapter, I also give a comprehensive review of diverse computational tools
employed in the scrutiny of protein-macromolecule interactions. Recent progress
in computational resources has expanded the number of tools available for study-
ing protein-macromolecule interactions at various molecular levels. These include
tools for predicting interacting residues from primary sequences, modeling protein-
macromolecule complexes, predicting hotspots in these complexes, and insights into
understanding the dynamics of their interactions. Here I present an overview of var-
ious computational tools to study different aspects of protein-protein and protein-
RNA interactions, with a focus on the overall application and development of the
field.
The second chapter of the thesis was dedicated to the exploration of inter-protein
bifurcated interactions. The study addressed the less-explored domain of interfa-
cial residues, i.e., inter-protein bifurcated interactions. While interfacial residues are
known to confer stability and specificity to these interactions, the extent of their
participation in inter-protein bifurcated interactions and the contribution of these
interactions is not well understood. This study highlighted the importance of these
interactions in multi-protein complexes.
Subsequently, the third chapter delved into the molecular intricacies of bacte-
rial two-component systems. Comprising sensor kinase and response regulator pro-
teins, these systems orchestrate bacterial responses to environmental fluctuations.
Predominantly characterized by cognate pairs, an intriguing phenomenon of non-
cognate interactions was observed in M. tuberculosis. This chapter is focused on the
structural basis and specificity of this atypical crosstalk.
The fourth chapter embarked on an exploration of the dynamic alterations within
the RNA polymerase complex upon interaction with RbpA. In the context of M. tu-
berculosis, the RNA polymerase (RNAP) complex encompasses subunits 2α, β, β’,
and ω. This complex further interacts with transcription activators and factors like
RbpA and CarD. This study was centered on unraveling the structural and dynamic
changes within the RNAP complex as it interacts with RbpA, DNA, and CarD. The
insights shed light on the intricate interplay among transcription factors during tran-
scription initiation, thus offering a lens into the regulatory mechanisms.
The fifth chapter ventured into the intricacies of the impact of mRNA on the
30S initiation complex and its preparatory role for interaction with the incoming
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50S subunit. Recognizing the regulatory role of mRNA in protein synthesis kinetics,
the research dissected the structural, mechanistic, and dynamic nuances of mRNA
recognition within the ribosome. This was accomplished through a comparative
analysis of ribosomal complexes in the presence and absence of mRNA. This study
highlighted the significance of mRNA binding in the ribosome complex and putative
allosteric sites I identified in regions away from mRNA binding sites in the complex.
This work provides fresh insights into mRNA association with the ribosome, high-
lighting changes in the interactions and dynamics of the ribosome assembly because
of the binding.
In the concluding chapter, an overall view of all the projects was provided. The
research spotlight was aimed at comprehending the intricate interplay of dynamics
within protein-macromolecule assemblies, particularly in the context of large com-
plexes. The thesis traversed diverse regions of computational analysis to elucidate
the roles played by various protein complexes in cellular functions. Through the
systematic exploration of protein dynamics, inter-protein interactions, bacterial two-
component systems, RNA polymerase dynamics, protein-RNA interactions, and ri-
bosomal responses to mRNA binding, the study deepened the understanding of
fundamental biological processes. | en_US |
