Browse
Submit Data
Databases
API
Help

Dataset Information

34 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals.

ABSTRACT: Bacterial microcompartments (BMCs) are large intracellular bodies that serve as simple organelles in many bacteria. They are proteinaceous structures composed of key enzymes encapsulated by a polyhedral protein shell. In previous studies, the organization of these large shells has been inferred from the conserved packing of the component shell proteins in two-dimensional (2D) layers within the context of three-dimensional (3D) crystals. Here, we show that well-ordered, 2D crystals of carboxysome shell proteins assemble spontaneously when His-tagged proteins bind to a monolayer of nickelated lipid molecules at an air-water interface. The molecular packing within the 2D crystals recapitulates the layered hexagonal sheets observed in 3D crystals. The results reinforce current models for the molecular design of BMC shells.

SUBMITTER: Dryden KA

PROVIDER: S-EPMC2821281 | biostudies-literature | 2009 Dec

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Publications

Two-dimensional crystals of carboxysome shell proteins recapitulate the hexagonal packing of three-dimensional crystals.

Dryden Kelly A KA Crowley Christopher S CS Tanaka Shiho S Yeates Todd O TO Yeager Mark M

Protein science : a publication of the Protein Society 20091201 12

Bacterial microcompartments (BMCs) are large intracellular bodies that serve as simple organelles in many bacteria. They are proteinaceous structures composed of key enzymes encapsulated by a polyhedral protein shell. In previous studies, the organization of these large shells has been inferred from the conserved packing of the component shell proteins in two-dimensional (2D) layers within the context of three-dimensional (3D) crystals. Here, we show that well-ordered, 2D crystals of carboxysome ...[more]

PMID: 19844993

Similar Datasets

Comparative analysis of carboxysome shell proteins.

Project description:Carboxysomes are metabolic modules for CO(2) fixation that are found in all cyanobacteria and some chemoautotrophic bacteria. They comprise a semi-permeable proteinaceous shell that encapsulates ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and carbonic anhydrase. Structural studies are revealing the integral role of the shell protein paralogs to carboxysome form and function. The shell proteins are composed of two domain classes: those with the bacterial microcompartment (BMC; Pfam00936) domain, which oligomerize to form (pseudo)hexamers, and those with the CcmL/EutN (Pfam03319) domain which form pentamers in carboxysomes. These two shell protein types are proposed to be the basis for the carboxysome's icosahedral geometry. The shell proteins are also thought to allow the flux of metabolites across the shell through the presence of the small pore formed by their hexameric/pentameric symmetry axes. In this review, we describe bioinformatic and structural analyses that highlight the important primary, tertiary, and quaternary structural features of these conserved shell subunits. In the future, further understanding of these molecular building blocks may provide the basis for enhancing CO(2) fixation in other organisms or creating novel biological nanostructures.

| S-EPMC3173617 | biostudies-literature

Insights from multiple structures of the shell proteins from the beta-carboxysome.

Project description:Carboxysomes are primitive bacterial organelles that function as a part of a carbon concentrating mechanism (CCM) under conditions where inorganic carbon is limiting. The carboxysome enhances the efficiency of cellular carbon fixation by encapsulating together carbonic anhydrase and the CO(2)-fixing enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). The carboxysome has a roughly icosahedral shape with an outer shell between 800 and 1500 A in diameter, which is constructed from a few thousand small protein subunits. In the cyanobacterium Synechocystis sp. PCC 6803, the previous structure determination of two homologous shell protein subunits, CcmK2 and CcmK4, elucidated how the outer shell is formed by the tight packing of CcmK hexamers into a molecular layer. Here we describe the crystal structure of the hexameric shell protein CcmK1, along with structures of mutants of both CcmK1 and CcmK2 lacking their sometimes flexible C-terminal tails. Variations in the way hexamers pack into layers are noted, while sulfate ions bound in pores through the layer provide further support for the hypothesis that the pores serve for transport of substrates and products into and out of the carboxysome. One of the new structures provides a high-resolution (1.3 A) framework for subsequent computational studies of molecular transport through the pores. Crystal and solution studies of the C-terminal deletion mutants demonstrate the tendency of the terminal segments to participate in protein--protein interactions, thereby providing a clue as to which side of the molecular layer of hexameric shell proteins is likely to face toward the carboxysome interior.

| S-EPMC2708042 | biostudies-literature

Spontaneous formation of two-dimensional and three-dimensional cholesterol crystals in single hydrated lipid bilayers.

Project description:Grazing incidence x-ray diffraction measurements were performed on single hydrated bilayers and monolayers of Ceramide/Cholesterol/1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocyholine at varying concentrations. There are substantial differences in the phase and structure behavior of the crystalline domains formed within the bilayers relative to the corresponding monolayers, due to interactions between the opposing lipid leaflets. Depending on the lipid composition, these interactions lead to phase separation and formation of cholesterol crystals. The cholesterol and ceramide/cholesterol mixed phases were further characterized at 37°C by immunolabeling with specific antibodies recognizing ordered molecular arrays of cholesterol. Previous studies have shown that cholesterol may nucleate in artificial membranes to form thick two-dimensional bilayer crystals. The study herein demonstrates further growth of cholesterol into three-dimensional crystals. We believe that these results may provide further insight into the formation of cholesterol crystals in early stages of atherosclerosis inflammation.

| S-EPMC3400773 | biostudies-literature

Self-assembly and modular functionalization of three-dimensional crystals from oppositely charged proteins.

Project description:Multicomponent crystals and nanoparticle superlattices are a powerful approach to integrate different materials into ordered nanostructures. Well-developed, especially DNA-based, methods for their preparation exist, yet most techniques concentrate on molecular and synthetic nanoparticle systems in non-biocompatible environment. Here we describe the self-assembly and characterization of binary solids that consist of crystalline arrays of native biomacromolecules. We electrostatically assembled cowpea chlorotic mottle virus particles and avidin proteins into heterogeneous crystals, where the virus particles adopt a non-close-packed body-centred cubic arrangement held together by avidin. Importantly, the whole preparation process takes place at room temperature in a mild aqueous medium allowing the processing of delicate biological building blocks into ordered structures with lattice constants in the nanometre range. Furthermore, the use of avidin-biotin interaction allows highly selective pre- or post-functionalization of the protein crystals in a modular way with different types of functional units, such as fluorescent dyes, enzymes and plasmonic nanoparticles.

| S-EPMC4109007 | biostudies-literature

Two-dimensional inorganic molecular crystals.

Project description:Two-dimensional molecular crystals, consisting of zero-dimensional molecules, are very appealing due to their novel physical properties. However, they are mostly limited to organic molecules. The synthesis of inorganic version of two-dimensional molecular crystals is still a challenge due to the difficulties in controlling the crystal phase and growth plane. Here, we design a passivator-assisted vapor deposition method for the growth of two-dimensional Sb2O3 inorganic molecular crystals as thin as monolayer. The passivator can prevent the heterophase nucleation and suppress the growth of low-energy planes, and enable the molecule-by-molecule lateral growth along high-energy planes. Using Raman spectroscopy and in situ transmission electron microscopy, we show that the insulating α-phase of Sb2O3 flakes can be transformed into semiconducting β-phase under heat and electron-beam irradiation. Our findings can be extended to the controlled growth of other two-dimensional inorganic molecular crystals and open up opportunities for potential molecular electronic devices.

| S-EPMC6797790 | biostudies-literature

Three-dimensional structure of the KdpFABC complex of Escherichia coli by electron tomography of two-dimensional crystals.

Project description:The KdpFABC complex (Kdp) functions as a K+ pump in Escherichia coli and is a member of the family of P-type ATPases. Unlike other family members, Kdp has a unique oligomeric composition and is notable for segregating K+ transport and ATP hydrolysis onto separate subunits (KdpA and KdpB, respectively). We have produced two-dimensional crystals of the KdpFABC complex within reconstituted lipid bilayers and determined its three-dimensional structure from negatively stained samples using a combination of electron tomography and real-space averaging. The resulting map is at a resolution of 2.4 nm and reveals a dimer of Kdp molecules as the asymmetric unit; however, only the cytoplasmic domains are visible due to the lack of stain penetration within the lipid bilayer. The sizes of these cytoplasmic domains are consistent with Kdp and, using a pseudo-atomic model, we have described the subunit interactions that stabilize the Kdp dimer within the larger crystallographic array. These results illustrate the utility of electron tomography in structure determination of ordered assemblies, especially when disorder is severe enough to hamper conventional crystallographic analysis.

| S-EPMC2322856 | biostudies-literature

Packing topology in crystals of proteins and small molecules: a comparison.

Project description:We compared the topologies of protein and small molecule crystals, which have many common features - both are molecular crystals with intermolecular interactions much weaker than intramolecular interactions. They also have different features - a considerably large fraction of the volume of protein crystals is occupied by liquid water while no room is available to other molecules in small molecule crystals. We analyzed the overall and local topology and performed multilevel topological analyses (with the software package ToposPro) of carefully selected high quality sets of protein and small molecule crystal structures. Given the suboptimal packing of protein crystals, which is due the special shape and size of proteins, it would be reasonable to expect that the topology of protein crystals is different from the topology of small molecule crystals. Surprisingly, we discovered that these two types of crystalline compounds have strikingly similar topologies. This might suggest that molecular crystal formations share symmetry rules independent of molecular dimension.

| S-EPMC5643379 | biostudies-literature

The diversity of three-dimensional photonic crystals.

Project description:Many butterflies, birds, beetles, and chameleons owe their spectacular colors to the microscopic patterns within their wings, feathers, or skin. When these patterns, or photonic crystals, result in the omnidirectional reflection of commensurate wavelengths of light, it is due to a complete photonic band gap (PBG). The number of natural crystal structures known to have a PBG is relatively small, and those within the even smaller subset of notoriety, including diamond and inverse opal, have proven difficult to synthesize. Here, we report more than 150,000 photonic band calculations for thousands of natural crystal templates from which we predict 351 photonic crystal templates - including nearly 300 previously-unreported structures - that can potentially be realized for a multitude of applications and length scales, including several in the visible range via colloidal self-assembly. With this large variety of 3D photonic crystals, we also revisit and discuss oft-used primary design heuristics for PBG materials.

| S-EPMC8100142 | biostudies-literature

Symmetry-enforced three-dimensional Dirac phononic crystals.

Project description:Dirac semimetals, the materials featuring fourfold degenerate Dirac points, are critical states of topologically distinct phases. Such gapless topological states have been accomplished by a band-inversion mechanism, in which the Dirac points can be annihilated pairwise by perturbations without changing the symmetry of the system. Here, we report an experimental observation of Dirac points that are enforced completely by the crystal symmetry using a nonsymmorphic three-dimensional phononic crystal. Intriguingly, our Dirac phononic crystal hosts four spiral topological surface states, in which the surface states of opposite helicities intersect gaplessly along certain momentum lines, as confirmed by additional surface measurements. The novel Dirac system may release new opportunities for studying elusive (pseudo) and offer a unique prototype platform for acoustic applications.

| S-EPMC7064592 | biostudies-literature

Characteristic boundaries associated with three-dimensional twins in hexagonal metals.

Project description:Twinning is a critically important deformation mode in hexagonal close-packed metals. Twins are three-dimensional (3D) domains, whose growth is mediated by the motion of facets bounding the 3D twin domains and influences work hardening in metals. An understanding of twin transformations therefore necessitates that the atomic-scale structure and intrinsic mobilities of facets be known and characterized. The present work addresses the former point by systematically characterizing the boundary structures of 3D {1¯012} twins in magnesium using high-resolution transmission electron microscopy (HRTEM). Eight characteristic facets associated with twin boundaries are reported, five of which have never been experimentally observed before. Further, molecular dynamics simulations suggest that the formation and motion of these facets is associated with the accumulation of twinning dislocations. This work provides insights into understanding the structural character of 3D twins and serves to develop strategies for modulating twin kinetics by modifying twin boundaries, such as solute segregation.

| S-EPMC7439641 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data