Conformational flexibility of the oncogenic protein LMO2 primes the formation of the multi-protein transcription complex

Abstract

LMO2 was discovered via chromosomal translocations in T-cell leukaemia and shown normally to be essential for haematopoiesis. LMO2 is made up of two LIM only domains (thus it is a LIM-only protein) and forms a bridge in a multi-protein complex. We have studied the mechanism of formation of this complex using a single domain antibody fragment that inhibits LMO2 by sequestering it in a non-functional form. The crystal structure of LMO2 with this antibody fragment has been solved revealing a conformational difference in the positioning and angle between the two LIM domains compared with its normal binding. This contortion occurs by bending at a central helical region of LMO2. This is a unique mechanism for inhibiting an intracellular protein function and the structural contusion implies a model in which newly synthesized, intrinsically disordered LMO2 binds to a partner protein nucleating further interactions and suggests approaches for therapeutic targeting of LMO2.

Intracellular immunization against HIV infection with an intracellular antibody that mimics HIV integrase binding to the cellular LEDGF protein

“…More striking is the observation that IBD is not bound by all three CDR loops, but lies alongside VH59 domain. This unusual antigen binding site is not unprecedented for VH complexes, and is similar to that observed for the complex between the anti-LMO2 VH576 and its LMO2 target 27 , where CDR3 is the only hypervariable loop involved, in addition to contacts within the VH framework amino acids. This is probably the result of the IAC screening procedure, where the VH59 protein sequence was derived from a diverse VH library with 14 amino acids of CDR3 randomized while CDR1 and CDR2 were not 16 .…”

The Structure of an LIM-Only Protein 4 (LMO4) and Deformed Epidermal Autoregulatory Factor-1 (DEAF1) Complex Reveals a Common Mode of Binding to LMO4

“…These values likely reflect local dynamics; for example, E98 and G105, which lie in a loop and a β-turn, respectively, exhibit low S 2 values. Collectively these data may report intrinsic flexibility within LIM domains (e.g., [68] , [69] , [70] ).…”

LMO2 at 25 years: a paradigm of chromosomal translocation proteins

“…The structure and conformational stabilization of LMO2 (green) when bound with LDB1-LID (purple) [ 15 ] is indicated in ( a ). When LMO2 (shown in blue in panel ( b )) is in complex with the anti-LMO2 VH (magenta), there is a conformational distortion, preventing nucleation of the LMO2-complex to the complex illustrated in ( d ) [ 49 ]. Superimposition of the normal LDB1- and VH-bound structures highlights the 23° contortion of the molecule when the anti-LMO2 VH is bound ( e ).…”

“…Superimposition of the normal LDB1- and VH-bound structures highlights the 23° contortion of the molecule when the anti-LMO2 VH is bound ( e ). The hinge region residue Phe88 (red), zinc atoms coordinated by the LIM-fingers (grey spheres) are indicated in both structures, drawn using UCSF Chimaera [ 14 ] from PDB accession codes 2XJY [ 15 ] and 4KFZ [ 49 ]. An in silico model of the structural effects on LMO2 induced by the peptide aptamer PA-207 is shown in ( c ).…”

“…The intracellular antibody fragments also abrogate the neoplastic effect of LMO2 in transgenic LMO2 cell transplantation assays [ 99 , 100 ] mediated by the disruption of the LMO2-complex by preventing LDB1 interaction [ 100 ]. The crystal structure of the LMO2 : VH complex [ 49 ], compared with that of LMO2-LDB1-LID fusion [ 15 ], demonstrates the mechanism. When the VH binds to LMO2, the latter adopts a distorted conformation around its hinge region ( figure 5 b , e ).…”