Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination

Abstract

Front cover:Surface representation of the protein-protein complexes of E2~Ub-TRIM E3 ligase, which I have embellished with interacting proteins/domains in a range of colors.The author apologizes to those whose work could not be cited directly as original research articles but rather cited the recent reviews, due to space limitations.All previously published original peer reviewed articles are reprinted with permissions from the publisher.© Copyright 2015 Madhanagopal Anandapadamanaban, unless otherwise mentioned. Linkoping studies in Science and Technology. Dissertation No. 1694 Printed in Sweden by LiU-Tryck, 2015 Madhanagopal Anandapadamanaban Structural insights into protein-protein interactions governing regulation in transcription initiation and ubiquitination AbstractVirtually every aspect of the cellular processes in eukaryotes requires that the interactions between protein molecules are well coordinated in different regulatory pathways. Any protein dysfunction involved in these regulatory pathways might lead to various pathological conditions. Understanding the structural and functional peculiarities of these proteins molecular machineries will help in formulating structure-based drug design.The first regulatory process studied here is the RNA polymerase-II mediated transcription of the eukaryotic protein-coding genes to produce mRNAs. This process requires the formation of the 'transcription initiation' by the assembly of Pre-Initiation Complex (PIC) formation at a core promoter region. Regulation at this initiation level is a key mechanism for the control of gene expression that governs cellular growth and differentiation. The transcription Factor IID (TFIID) is a conserved multiprotein general transcription factor with an essential role in nucleating the PIC formation, composed of TATA Binding Protein (TBP) and about 14 TBP Associated Factors (TAFs). The here presented crystal structure (1.97 Å) of TBP bound to TAND1 and TAND2 domains from TAF1 reveals a detailed molecular pattern of interactions involving both transcriptionally activating and repressing regions in TBP, thereby uncovering central principles for anchoring of TBP-binding motifs. Together with NMR and cellular analysis, this work provides the structural basis of competitive binding with TFIIA to modulate TBP in promoter recognition.In eukaryotes, another fundamental mechanism in the regulation of cellular physiology is the post-translational modification of substrate proteins by ubiquitin, termed 'ubiquitination'. Important actors in this mechanism are the ubiquitin-ligases (E3s) that culminate the transfer of ubiquitin to the substrate and govern the specificity of this system. One E3 ligase in particular, TRIM21, defines a subgroup of the Tripartite Motif (TRIM) family, which belongs to the major RING-type of E3 ubiquitin ligases, and plays an important role in pathogenesis of autoimmunity by mediating ubiquitination of transcription factors. The crystal structure (2.86 Å) of the RING domain from TRIM21 ...