The low-resolution 3D-structure of porin, a channel-forming protein in E. coliouter membranes

1983 ◽  
Vol 41 ◽  
pp. 440-441
Author(s):  
A. Engel ◽  
D.L. Dorset ◽  
A. Massalski ◽  
J.P. Rosenbusch
Keyword(s):  
Crystal Packing ◽  
3D Structure ◽  
Gram Negative Bacteria ◽  
Protein Ratio ◽  
Crystal Forms ◽  
Large Molecules ◽  
Functional Studies ◽  
Voltage Dependent ◽  
Planar Membranes ◽  
Hexagonal Arrays

Porins represent a group of channel forming proteins that facilitate diffusion of small solutes across the outer membrane of Gram-negative bacteria, while excluding large molecules (>650 Da). Planar membranes reconstituted from purified matrix porin (OmpF protein) trimers and phospholipids have allowed quantitative functional studies of the voltage-dependent channels and revealed concerted activation of triplets. Under the same reconstitution conditions but using high protein concentrations porin aggregated to 2D lattices suitable for electron microscopy and image processing. Depending on the lipid-to- protein ratio three different crystal packing arrangements were observed: a large (a = 93 Å) and a small (a = 79 Å) hexagonal and a rectangular (a = 79 Å b = 139 Å) form with p3 symmetry for the hexagonal arrays. In all crystal forms distinct stain filled triplet indentations could be seen and were found to be morphologically identical within a resolution of (22 Å). It is tempting to correlate stain triplets with triple channels, but the proof of this hypothesis requires an analysis of the structure in 3 dimensions.

scholarly journals Conformational changes in Apolipoprotein N-acyltransferase (Lnt)

2018 ◽  
Author(s):  
Benjamin Wiseman ◽  
Martin Högbom
Keyword(s):  
Conformational Changes ◽  
Crystal Packing ◽  
Cell Envelope ◽  
Crystal Form ◽  
Covalent Attachment ◽  
Gram Negative Bacteria ◽  
Asymmetric Unit ◽  
Cellular Functions ◽  
Crystal Forms ◽  
Potential Mode

SUMMARYIn bacteria, lipoproteins are important components of the cell envelope and are responsible for many essential cellular functions. They are produced by the post-translational covalent attachment of lipids that occurs via a sequential 3-step process controlled by three essential integral membrane enzymes. The last step of this process, unique to Gram negative bacteria, is the N-acylation of the terminal cysteine by Apolipoprotein N-acyltransferase (Lnt) to form the final mature lipoprotein. Here we report 2 crystal forms of this enzyme. In one form the enzyme crystallized with two molecules in the asymmetric unit. In one of those molecules the thioester acyl-intermediate is observed. In the other molecule, the crystal packing suggests one potential mode of apolipoprotein docking to Lnt. In the second crystal form the enzyme crystallized with one molecule in the asymmetric unit in an apparent apo-state remarkably devoid of any bound molecules in the large open substrate entry portal. Taken together, these structures suggest that the movement of the essential W237 is triggered by substrate binding and could help direct and stabilize the interaction between Lnt and the incoming substrate apolipoprotein.Graphical Abstract

scholarly journals Characterization of a porin channel in the endosymbiont of the trypanosomatid protozoan Crithidia deanei

Microbiology ◽  
2011 ◽  
Vol 157 (10) ◽  
pp. 2818-2830 ◽  
Author(s):  
Iamara da Silva Andrade ◽  
João Lídio Vianez-Júnior ◽  
Carolina Lage Goulart ◽  
Fabrice Homblé ◽  
Jean-Marie Ruysschaert ◽  
...  
Keyword(s):  
3D Structure ◽  
Symbiotic Bacterium ◽  
Gram Negative Bacteria ◽  
Genome Database ◽  
Gram Negative ◽  
Secondary Structure Analysis ◽  
Electrophysiological Measurements ◽  
Mutualistic Relationship ◽  
Obligate Intracellular Bacteria

Crithidia deanei is a trypanosomatid protozoan that harbours a symbiotic bacterium. The partners maintain a mutualistic relationship, thus constituting an excellent model for studying metabolic exchanges between the host and the symbiont, the origin of organelles and cellular evolution. According to molecular analysis, symbionts of different trypanosomatid species share high identity and descend from a common ancestor, a β-proteobacterium of the genus Bordetella. The endosymbiont is surrounded by two membranes, like Gram-negative bacteria, but its envelope presents special features, since phosphatidylcholine is a major membrane component and the peptidoglycan layer is highly reduced, as described in other obligate intracellular bacteria. Like the process that generated mitochondria and plastids, the endosymbiosis in trypanosomatids depends on pathways that facilitate the intensive metabolic exchanges between the bacterium and the host protozoan. A search of the annotated symbiont genome database identified one sequence with identity to porin-encoding genes of the genus Bordetella. Considering that the symbiont outer membrane has a great accessibility to cytoplasm host factors, it was important to characterize this single porin-like protein using biochemical, molecular, computational and ultrastructural approaches. Antiserum against the recombinant porin-like molecule revealed that it is mainly located in the symbiont envelope. Secondary structure analysis and comparative modelling predicted the protein 3D structure as an 18-domain β-barrel, which is consistent with porin channels. Electrophysiological measurements showed that the porin displays a slight preference for cations over anions. Taken together, the data presented herein suggest that the C. deanei endosymbiont porin is phylogenetically and structurally similar to those described in Gram-negative bacteria, representing a diffusion channel that might contribute to the exchange of nutrients and metabolic precursors between the symbiont and its host cell.

scholarly journals On the Architecture of the Gram-Negative Bacterial Murein Sacculus

2000 ◽  
Vol 182 (20) ◽  
pp. 5925-5930 ◽  
Author(s):  
David Pink ◽  
Jeremy Moeller ◽  
Bonnie Quinn ◽  
Manfred Jericho ◽  
Terry Beveridge
Keyword(s):  
Gram Negative Bacteria ◽  
Defect Structures ◽  
Waste Products ◽  
Gram Negative ◽  
Large Molecules ◽  
Glycan Chain ◽  
Pass Through ◽  
Murein Sacculus ◽  
Chain Lengths ◽  
Peptidoglycan Layer

ABSTRACT The peptidoglycan network of the murein sacculus must be porous so that nutrients, waste products, and secreted proteins can pass through. Using Escherichia coli and Pseudomonas aeruginosa as a baseline for gram-negative sacculi, the hole size distribution in the peptidoglycan network has been modeled by computer simulation to deduce the network's properties. By requiring that the distribution of glycan chain lengths predicted by the model be in accord with the distribution observed, we conclude that the holes are slits running essentially perpendicular to the local axis of the glycan chains (i.e., the slits run along the long axis of the cell). This result is in accord with previous permeability measurements of Beveridge and Jack and Demchik and Koch. We outline possible advantages that might accrue to the bacterium via this architecture and suggest ways in which such defect structures might be detected. Certainly, large molecules do penetrate the peptidoglycan layer of gram-negative bacteria, and the small slits that we suggest might be made larger by the bacterium.

Crystal packing in six crystal forms of pancreatic ribonuclease

1992 ◽  
Vol 228 (1) ◽  
pp. 243-251 ◽  
Author(s):  
Marie-Pierre Crosio ◽  
Joël Janin ◽  
Magali Jullien
Keyword(s):  
Crystal Packing ◽  
Crystal Forms ◽  
Pancreatic Ribonuclease

Nogo Receptor crystal structures with a native disulfide pattern suggest a novel mode of self-interaction

2017 ◽  
Vol 73 (11) ◽  
pp. 860-876 ◽  
Author(s):  
Matti F. Pronker ◽  
Roderick P. Tas ◽  
Hedwich C. Vlieg ◽  
Bert J. C. Janssen
Keyword(s):  
Crystal Structures ◽  
Disulfide Bonds ◽  
Crystal Packing ◽  
Surface Protein ◽  
Terminal Segment ◽  
Structural Basis ◽  
Crystal Forms ◽  
Nogo Receptor ◽  
Terminal Loop ◽  
Lrr Domain

The Nogo Receptor (NgR) is a glycophosphatidylinositol-anchored cell-surface protein and is a receptor for three myelin-associated inhibitors of regeneration: myelin-associated glycoprotein, Nogo66 and oligodendrocyte myelin glycoprotein. In combination with different co-receptors, NgR mediates signalling that reduces neuronal plasticity. The available structures of the NgR ligand-binding leucine-rich repeat (LRR) domain have an artificial disulfide pattern owing to truncated C-terminal construct boundaries. NgR has previously been shown to self-associateviaits LRR domain, but the structural basis of this interaction remains elusive. Here, crystal structures of the NgR LRR with a longer C-terminal segment and a native disulfide pattern are presented. An additional C-terminal loop proximal to the C-terminal LRR cap is stabilized by two newly formed disulfide bonds, but is otherwise mostly unstructured in the absence of any stabilizing interactions. NgR crystallized in six unique crystal forms, three of which share a crystal-packing interface. NgR crystal-packing interfaces from all eight unique crystal forms are compared in order to explore how NgR could self-interact on the neuronal plasma membrane.

scholarly journals Structure of the human voltage-dependent anion channel

2008 ◽  
Vol 105 (40) ◽  
pp. 15370-15375 ◽  
Author(s):  
Monika Bayrhuber ◽  
Thomas Meins ◽  
Michael Habeck ◽  
Stefan Becker ◽  
Karin Giller ◽  
...  
Keyword(s):  
Metabolic Flux ◽  
3D Structure ◽  
Anion Channel ◽  
Bioinformatic Analysis ◽  
Mitochondrial Outer Membrane ◽  
Voltage Dependent Anion Channel ◽  
X Ray Crystallography ◽  
Voltage Dependent ◽  
Α Helix ◽  
Induced Apoptosis

The voltage-dependent anion channel (VDAC), also known as mitochondrial porin, is the most abundant protein in the mitochondrial outer membrane (MOM). VDAC is the channel known to guide the metabolic flux across the MOM and plays a key role in mitochondrially induced apoptosis. Here, we present the 3D structure of human VDAC1, which was solved conjointly by NMR spectroscopy and x-ray crystallography. Human VDAC1 (hVDAC1) adopts a β-barrel architecture composed of 19 β-strands with an α-helix located horizontally midway within the pore. Bioinformatic analysis indicates that this channel architecture is common to all VDAC proteins and is adopted by the general import pore TOM40 of mammals, which is also located in the MOM.

scholarly journals Crystal chemistry and photomechanical behavior of 3,4-dimethoxycinnamic acid: correlation between maximum yield in the solid-state topochemical reaction and cooperative molecular motion

IUCrJ ◽  
2015 ◽  
Vol 2 (6) ◽  
pp. 653-660 ◽  
Author(s):  
Manish Kumar Mishra ◽  
Arijit Mukherjee ◽  
Upadrasta Ramamurty ◽  
Gautam R. Desiraju
Keyword(s):  
Solid State ◽  
Crystal Packing ◽  
Maximum Yield ◽  
Structure Property ◽  
Crystal Forms ◽  
Individual Crystal ◽  
Structure Property Relationships ◽  
Molecular Movement ◽  
Truxillic Acid ◽  
The Individual

A new monoclinic polymorph, form II (P21/c,Z= 4), has been isolated for 3,4-dimethoxycinnamic acid (DMCA). Its solid-state 2 + 2 photoreaction to the corresponding α-truxillic acid is different from that of the first polymorph, the triclinic form I (P\bar 1,Z= 4) that was reported in 1984. The crystal structures of the two forms are rather different. The two polymorphs also exhibit different photomechanical properties. Form I exhibits photosalient behavior but this effect is absent in form II. These properties can be explained on the basis of the crystal packing in the two forms. The nanoindentation technique is used to shed further insights into these structure−property relationships. A faster photoreaction in form I and a higher yield in form II are rationalized on the basis of the mechanical properties of the individual crystal forms. It is suggested that both Schmidt-type and Kaupp-type topochemistry are applicable for the solid-statetrans-cinnamic acid photodimerization reaction. Form I of DMCA is more plastic and seems to react under Kaupp-type conditions with maximum molecular movements. Form II is more brittle, and its interlocked structure seems to favor Schmidt-type topochemistry with minimum molecular movement.

Sign in / Sign up

Export Citation Format

Share Document