Molecular Interactions Driving Intermediate Filament Assembly

Abstract

Given the role of intermediate filaments (IFs) in normal cell physiology and scores of IF-linked diseases, the importance of understanding their molecular structure is beyond doubt. Research into the IF structure was initiated more than 30 years ago, and some important advances have been made. Using crystallography and other methods, the central coiled-coil domain of the elementary dimer and also the structural basis of the soluble tetramer formation have been studied to atomic precision. However, the molecular interactions driving later stages of the filament assembly are still not fully understood. For cytoplasmic IFs, much of the currently available insight is due to chemical cross-linking experiments that date back to the 1990s. This technique has since been radically improved, and several groups have utilized it recently to obtain data on lamin filament assembly. Here, we will summarize these findings and reflect on the remaining open questions and challenges of IF structure. We argue that, in addition to X-ray crystallography, chemical cross-linking and cryoelectron microscopy are the techniques that should enable major new advances in the field in the near future.

In Silico and In Vivo Analysis of Amino Acid Substitutions That Cause Laminopathies

“…The wild-type lamin A/C dimer structure predictions compare well with the experimentally derived structure of a lamin A/C dimer [74]. The AlphaFold v2.0-predicted extended dimer structure shows concordance with the experimental model [74]. The Al-phaFold v2.0 bent structure shows a region of disorder that corresponds to a disordered region in the experimental model, consistent with conformational flexibility.…”

“…The wild-type lamin A/C dimer structure predictions compare well with the experimentally derived structure of a lamin A/C dimer [74]. The AlphaFold v2.0-predicted extended dimer structure shows concordance with the experimental model [74].…”

Impact of N-Terminal Tags on De Novo Vimentin Intermediate Filament Assembly

“…Each vimentin monomer contains a highly conserved central α-helical rod domain of 312 residues, flanked by non-helical head (N-terminal) and tail (C-terminal) domains. The rod domain is further split into 1A, 1B (together forming coil 1), 2A and 2B (together forming coil 2) α-helical segments that are interspaced by L1, L12 and L2 linkers [ 13 , 14 , 15 ], although recent literature on the subject has challenged the existence of linker L2 [ 16 ]. Towards the C-terminus of coil 2 at position 350 there is a highly conserved region called ‘stutter’ causing discontinuity in the heptad repeats [ 17 ].…”

Cyclin-dependent kinase 1 depolymerizes nuclear lamin filaments by disrupting the head-to-tail interaction of the lamin central rod domain

“…Four types of dimer-to-dimer interaction modes (A11, A22, A12, and ACN) have been observed in IFs when forming the mature filament (6,15,16). The lamin filament model was proposed using three types of interaction modes (A11, A22, and ACN) based on the cryo-ET and chemical cross-linking data (7,(17)(18)(19). They further proposed that four or more units of the 3.5-nm thick filaments are laterally assembled into 10-nm-thick filaments of cytosolic IFs in the A12 interaction mode.…”

“…The structure of the long lamin A/C fragment (residues 1-300) has been shown to have J o u r n a l P r e -p r o o f 4 an antiparallel arrangement of two parallel coiled-coil dimers at 3.2 Å resolution (7). This antiparallel arrangement of lamins was designated as the 'A11' interaction, previously named due to the antiparallel interaction between the coil 1b regions from the adjacent coiled-coil dimers (1,17). The A11 tetramers, formed by the A11 interaction, are further joined to elongate the linear filament by another interaction mode, A22, representing an antiparallel arrangement between the coil 2 regions (15,20).…”