Location‐Dependent Lanthanide Selectivity Engineered into Structurally Characterized Designed Coiled Coils

The cytoskeleton of the eukaryotic cell provides a structural and functional scaffold enabling biochemical and cellular functions. While actin and microtubules form the main framework of the cell, intermediate filament networks provide unique mechanical properties that increase the resilience of both the cytoplasm and the nucleus, thereby maintaining cellular function while under mechanical pressure. Intermediate filaments (IFs) are imperative to a plethora of regulatory and signaling functions in mechanotransduction. Mutations in all types of IF proteins are known to affect the architectural integrity and function of cellular processes, leading to debilitating diseases. The basic building block of all IFs are elongated α-helical coiled-coils that assemble hierarchically into complex meshworks. A remarkable mechanical feature of IFs is the capability of coiled-coils to metamorphize into β-sheets under stress, making them one of the strongest and most resilient mechanical entities in nature. Here, we discuss structural and mechanical aspects of IFs with a focus on nuclear lamins and vimentin.

Download Full-text

SNAP-25, a t-SNARE which binds to both syntaxin and synaptobrevin via domains that may form coiled coils.

Journal of Biological Chemistry ◽

10.1016/s0021-9258(18)47003-2 ◽

1994 ◽

Vol 269 (44) ◽

pp. 27427-27432 ◽

Cited By ~ 1

Author(s):

E R Chapman ◽

S An ◽

N Barton ◽

R Jahn

Keyword(s):

Coiled Coils

Download Full-text

Stereochemical considerations for constructing α-helical protein bundles with particular application to membrane proteins

Biochemical Journal ◽

10.1042/bj1630045 ◽

1977 ◽

Vol 163 (1) ◽

pp. 45-57 ◽

Cited By ~ 24

Author(s):

A K Dunker ◽

D J Zaleske

Keyword(s):

Membrane Proteins ◽

Coiled Coils ◽

Alpha Helices ◽

Helical Protein

The stereochemical constraints originally used to construct two- and three-stranded alpha-helical coiled-coils were generalized for aggregates of alpha-helices containing from 4 to 14 alpha-helices in tubular bundles. Certain features of bacteriorhodopsin show excellent correlations with these stereochemical constraints.

Download Full-text

De novo predictions of the quaternary structure of leucine zippers and other coiled coils

International Journal of Quantum Chemistry ◽

10.1002/(sici)1097-461x(1999)75:3<165::aid-qua6>3.0.co;2-q ◽

1999 ◽

Vol 75 (3) ◽

pp. 165-176 ◽

Cited By ~ 2

Author(s):

Jeffrey Skolnick ◽

Andrzej Kolinski ◽

Debasisa Mohanty

Keyword(s):

Quaternary Structure ◽

De Novo ◽

Coiled Coils ◽

Leucine Zippers

Download Full-text

Coiled-coil networking shapes cell molecular machinery

Molecular Biology of the Cell ◽

10.1091/mbc.e12-05-0396 ◽

2012 ◽

Vol 23 (19) ◽

pp. 3911-3922 ◽

Cited By ~ 44

Author(s):

Yongqiang Wang ◽

Xinlei Zhang ◽

Hong Zhang ◽

Yi Lu ◽

Haolong Huang ◽

...

Keyword(s):

Protein Interactions ◽

Critical Role ◽

Coiled Coil ◽

Coiled Coils ◽

Protein Protein Interactions ◽

Full Spectrum ◽

Kinetochore Assembly ◽

Genome Wide ◽

Molecular Machinery ◽

Systematic Understanding

The highly abundant α-helical coiled-coil motif not only mediates crucial protein–protein interactions in the cell but is also an attractive scaffold in synthetic biology and material science and a potential target for disease intervention. Therefore a systematic understanding of the coiled-coil interactions (CCIs) at the organismal level would help unravel the full spectrum of the biological function of this interaction motif and facilitate its application in therapeutics. We report the first identified genome-wide CCI network in Saccharomyces cerevisiae, which consists of 3495 pair-wise interactions among 598 predicted coiled-coil regions. Computational analysis revealed that the CCI network is specifically and functionally organized and extensively involved in the organization of cell machinery. We further show that CCIs play a critical role in the assembly of the kinetochore, and disruption of the CCI network leads to defects in kinetochore assembly and cell division. The CCI network identified in this study is a valuable resource for systematic characterization of coiled coils in the shaping and regulation of a host of cellular machineries and provides a basis for the utilization of coiled coils as domain-based probes for network perturbation and pharmacological applications.

Download Full-text

The Structure of BRMS1 Nuclear Export Signal and SNX6 Interacting Region Reveals a Hexamer Formed by Antiparallel Coiled Coils

Journal of Molecular Biology ◽

10.1016/j.jmb.2011.07.006 ◽

2011 ◽

Vol 411 (5) ◽

pp. 1114-1127 ◽

Cited By ~ 9

Author(s):

Mercedes Spínola-Amilibia ◽

José Rivera ◽

Miguel Ortiz-Lombardía ◽

Antonio Romero ◽

José L. Neira ◽

...

Keyword(s):

Nuclear Export ◽

Nuclear Export Signal ◽

Coiled Coils ◽

Export Signal

Download Full-text

Structural features and functional domains of amassin-1, a cell-binding olfactomedin protein

Biochemistry and Cell Biology ◽

10.1139/o07-055 ◽

2007 ◽

Vol 85 (5) ◽

pp. 552-562 ◽

Cited By ~ 9

Author(s):

Brian J. Hillier ◽

Victor D. Vacquier

Keyword(s):

Disulfide Bonds ◽

Biological Activities ◽

Structural Features ◽

Body Cavity ◽

Binding Activity ◽

Coiled Coils ◽

Cell Binding ◽

Calcium Dependent ◽

Dependent Cell ◽

A Cell

Amassin-1 mediates a rapid cell adhesion that tightly adheres sea urchin coelomocytes (body cavity immunocytes) together. Three major structural regions exist in amassin-1: a short β region, 3 coiled coils, and an olfactomedin domain. Amassin-1 contains 8 disulfide-bonded cysteines that, upon reduction, render it inactive. Truncated forms of recombinant amassin-1 were expressed and purified from Pichia pastoris and their disulfide bonding and biological activities investigated. Expressed alone, the olfactomedin domain contained 2 intramolecular disulfide bonds, existed in a monomeric state, and inhibited amassin-1-mediated clotting of coelomocytes by a calcium-dependent cell-binding activity. The N-terminal β region, containing 3 cysteines, was not required for clotting activity. The coiled coils may dimerize amassin-1 in a parallel orientation through a homodimerizing disulfide bond. Neither amassin-1 fragments that were disulfide-linked as dimers or that were engineered to exist as dimers induced coelomocytes clotting. Clotting required higher multimeric states of amassin-1, possibly tetramers, which occurred through the N-terminal β region and (or) the first segment of coiled coils.

Download Full-text

ARCIMBOLDOon coiled coils

Acta Crystallographica Section D Structural Biology ◽

10.1107/s2059798317017582 ◽

2018 ◽

Vol 74 (3) ◽

pp. 194-204 ◽

Cited By ~ 14

Author(s):

Iracema Caballero ◽

Massimo Sammito ◽

Claudia Millán ◽

Andrey Lebedev ◽

Nicolas Soler ◽

...

Keyword(s):

Coiled Coil ◽

Coiled Coils ◽

Translational Symmetry ◽

Command Line ◽

Phase Problem ◽

Final Solution ◽

Resolution Limit ◽

Helical Structures ◽

Small Model ◽

Test Pool

ARCIMBOLDOsolves the phase problem by combining the location of small model fragments usingPhaserwith density modification and autotracing usingSHELXE. Mainly helical structures constitute favourable cases, which can be solved using polyalanine helical fragments as search models. Nevertheless, the solution of coiled-coil structures is often complicated by their anisotropic diffraction and apparent translational noncrystallographic symmetry. Long, straight helices have internal translational symmetry and their alignment in preferential directions gives rise to systematic overlap of Patterson vectors. This situation has to be differentiated from the translational symmetry relating different monomers.ARCIMBOLDO_LITEhas been run on single workstations on a test pool of 150 coiled-coil structures with 15–635 amino acids per asymmetric unit and with diffraction data resolutions of between 0.9 and 3.0 Å. The results have been used to identify and address specific issues when solving this class of structures usingARCIMBOLDO. Features fromPhaserv.2.7 onwards are essential to correct anisotropy and produce translation solutions that will pass the packing filters. As the resolution becomes worse than 2.3 Å, the helix direction may be reversed in the placed fragments. Differentiation between true solutions and pseudo-solutions, in which helix fragments were correctly positioned but in a reverse orientation, was found to be problematic at resolutions worse than 2.3 Å. Therefore, after every new fragment-placement round, complete or sparse combinations of helices in alternative directions are generated and evaluated. The final solution is once again probed by helix reversal, refinement and extension. To conclude, density modification andSHELXEautotracing incorporating helical constraints is also exploited to extend the resolution limit in the case of coiled coils and to enhance the identification of correct solutions. This study resulted in a specialized mode withinARCIMBOLDOfor the solution of coiled-coil structures, which overrides the resolution limit and can be invoked from the command line (keyword coiled_coil) orARCIMBOLDO_LITEtask interface inCCP4i.

Download Full-text

Bioelectrocatalytic hydrogels from electron-conducting metallopolypeptides coassembled with bifunctional enzymatic building blocks

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.0805249105 ◽

2008 ◽

Vol 105 (40) ◽

pp. 15275-15280 ◽

Cited By ~ 56

Author(s):

Ian R. Wheeldon ◽

Joshua W. Gallaway ◽

Scott Calabrese Barton ◽

Scott Banta

Keyword(s):

Polyphenol Oxidase ◽

Building Block ◽

Leucine Zipper ◽

Electrical Contact ◽

Building Blocks ◽

Coiled Coils ◽

Biofuel Cell ◽

Random Coil ◽

Catalytic Current ◽

And Function

Here, we present two bifunctional protein building blocks that coassemble to form a bioelectrocatalytic hydrogel that catalyzes the reduction of dioxygen to water. One building block, a metallopolypeptide based on a previously designed triblock polypeptide, is electron-conducting. A second building block is a chimera of artificial α-helical leucine zipper and random coil domains fused to a polyphenol oxidase, small laccase (SLAC). The metallopolypeptide has a helix–random-helix secondary structure and forms a hydrogel via tetrameric coiled coils. The helical and random domains are identical to those fused to the polyphenol oxidase. Electron-conducting functionality is derived from the divalent attachment of an osmium bis-bipyrdine complex to histidine residues within the peptide. Attachment of the osmium moiety is demonstrated by mass spectroscopy (MS-MALDI-TOF) and cyclic voltammetry. The structure and function of the α-helical domains are confirmed by circular dichroism spectroscopy and by rheological measurements. The metallopolypeptide shows the ability to make electrical contact to a solid-state electrode and to the redox centers of modified SLAC. Neat samples of the modified SLAC form hydrogels, indicating that the fused α-helical domain functions as a physical cross-linker. The fusion does not disrupt dimer formation, a necessity for catalytic activity. Mixtures of the two building blocks coassemble to form a continuous supramolecular hydrogel that, when polarized, generates a catalytic current in the presence of oxygen. The specific application of the system is a biofuel cell cathode, but this protein-engineering approach to advanced functional hydrogel design is general and broadly applicable to biocatalytic, biosensing, and tissue-engineering applications.

Download Full-text