A systematic structural comparison of all solved small proteins deposited in PDB. The effect of disulfide bonds in protein fold

Defensins are small proteins, usually ranging from 4 to 6 kDa, amphipathic, disulfide-rich, and with a small or even absent hydrophobic core. Since a hydrophobic core is generally found in globular proteins that fold in an aqueous solvent, the peculiar fold of defensins can challenge tertiary protein structure predictors. We performed a PDB-wide survey of small proteins (4-6 kDa) to understand the similarities of defensins with other small disulfide-rich proteins. We found no differences when we compared defensins with non-defensins regarding the proportion and exposition to the solvent of apolar, polar, and charged residues. Then we divided all small proteins (4-6 kDa) deposited in PDB into two groups, one group with at least one disulfide bond (bonded, defensins included) and another group without any disulfide bond (unbonded). The group of bonded proteins presented apolar residues more exposed to the solvent than the unbonded group. The ab initio algorithm for tertiary protein structure prediction Robetta was more accurate to predict unbonded than bonded proteins. Our work highlights one more layer of complexity for the tertiary protein prediction structure: small disulfide-rich proteins' ability to fold even with a poor hydrophobic core.

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Structure of a DsbF homologue fromCorynebacterium diphtheriae

Acta Crystallographica Section F Structural Biology Communications ◽

10.1107/s2053230x14016355 ◽

2014 ◽

Vol 70 (9) ◽

pp. 1167-1172 ◽

Cited By ~ 3

Author(s):

Si-Hyeon Um ◽

Jin-Sik Kim ◽

Kangseok Lee ◽

Nam-Chul Ha

Keyword(s):

Active Site ◽

Disulfide Bonds ◽

Bond Formation ◽

Extracellular Proteins ◽

Disulfide Bond Formation ◽

Gram Negative Bacteria ◽

Structural Comparison ◽

Positive Bacterium ◽

E Coli

Disulfide-bond formation, mediated by the Dsb family of proteins, is important in the correct folding of secreted or extracellular proteins in bacteria. In Gram-negative bacteria, disulfide bonds are introduced into the folding proteins in the periplasm by DsbA. DsbE fromEscherichia colihas been implicated in the reduction of disulfide bonds in the maturation of cytochromec. The Gram-positive bacteriumMycobacterium tuberculosisencodes DsbE and its homologue DsbF, the structures of which have been determined. However, the two mycobacterial proteins are able to oxidatively fold a proteinin vitro, unlike DsbE fromE. coli. In this study, the crystal structure of a DsbE or DsbF homologue protein fromCorynebacterium diphtheriaehas been determined, which revealed a thioredoxin-like domain with a typical CXXC active site. Structural comparison withM. tuberculosisDsbF would help in understanding the function of theC. diphtheriaeprotein.

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Cryo-electron microscopy of two-dimensional crystals of reduced type B botulinum neurotoxin

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100123052 ◽

1992 ◽

Vol 50 (1) ◽

pp. 530-531

Author(s):

P. F. Flicker ◽

V.S. Kulkarni ◽

J. P. Robinson ◽

G. Stubbs ◽

B. R. DasGupta

Keyword(s):

Disulfide Bonds ◽

Clostridium Botulinum ◽

Structural Changes ◽

Two Dimensional ◽

Type B ◽

Single Chain ◽

Muscle Paralysis ◽

Cryo Electron Microscopy ◽

Disulfide Linkages ◽

Intracellular Action

Botulinum toxin is a potent neurotoxin produced by Clostridium botulinum. The toxin inhibits release of neurotransmitter, causing muscle paralysis. There are several serotypes, A to G, all of molecular weight about 150,000. The protein exists as a single chain or or as two chains, with two disulfide linkages. In a recent investigation on intracellular action of neurotoxins it was reported that type B neurotoxin can inhibit the release of Ca++-activated [3H] norepinephrine only if the disulfide bonds are reduced. In order to investigate possible structural changes in the toxin upon reduction of the disulfide bonds, we have prepared two-dimensional crystals of reduced type B neurotoxin. These two-dimensional crystals will be compared with those of the native (unreduced) type B toxin.

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Use of Antibody to aid Visualization of Protein at the Termini of Bacteriophage Ø29 DNA

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s1431927600002385 ◽

1980 ◽

Vol 38 ◽

pp. 540-541

Author(s):

Dwight Anderson ◽

Charlene Peterson ◽

Gursaran Notani ◽

Bernard Reilly

Keyword(s):

Electron Microscopy ◽

Bacillus Subtilis ◽

Dna Synthesis ◽

Restriction Endonuclease ◽

Protein Complex ◽

Protein Product ◽

Viral Dna ◽

Small Proteins ◽

Antibody Labeling ◽

Subtilis Bacteriophage

The protein product of cistron 3 of Bacillus subtilis bacteriophage Ø29 is essential for viral DNA synthesis and is covalently bound to the 5’-termini of the Ø29 DNA. When the DNA-protein complex is cleaved with a restriction endonuclease, the protein is bound to the two terminal fragments. The 28,000 dalton protein can be visualized by electron microscopy as a small dot and often is seen only when two ends are in apposition as in multimers or in glutaraldehyde-fixed aggregates. We sought to improve the visibility of these small proteins by use of antibody labeling.

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Specific Cross-reaction of IgG Anti-phospholipid Antibody with Platelet Glycoprotein IIIa

Thrombosis and Haemostasis ◽

10.1055/s-0038-1650238 ◽

1996 ◽

Vol 75 (01) ◽

pp. 168-174 ◽

Cited By ~ 13

Author(s):

Shigeru Tokita ◽

Morio Arai ◽

Naomasa Yamamoto ◽

Yasuhiro Katagiri ◽

Kenjiro Tanoue ◽

...

Keyword(s):

Platelet Aggregation ◽

Heparan Sulfate ◽

Disulfide Bonds ◽

Dextran Sulfate ◽

Human Platelets ◽

Platelet Glycoprotein ◽

Activated Platelets ◽

Fibrinogen Binding ◽

Dose Dependent Fashion ◽

Glycoprotein Iiia

SummaryTo study the pathological functions of anti-phospholipid (anti-PL) antibodies, we have analyzed their effect on platelet function. We identified an IgG anti-PL mAb, designated PSG3, which cross-reacted specifically with glycoprotein (GP) IIIa in human platelets and inhibited platelet aggregation. PSG3 bound also to certain polyanionic substances, such as double-stranded DNA, heparan sulfate, dextran sulfate and acetylated-LDL, but not to other polyanionic substances. The binding of PSG3 to GPIIIa was completely inhibited by heparan sulfate and dextran sulfate, indicating that PSG3 recognizes a particular array of negative charges expressed on both GPIIIa and the specified polyanionic substances. Since neither neuraminidase- nor endoglycopeptidase F-treatment of GPIIIa had any significant effect on the binding of PSG3, this array must be located within the amino acid sequence of GPIIIa but not in the carbohydrate moiety. Reduction of the disulfide bonds in GPIIIa greatly reduced its reactivity, suggesting that the negative charges in the epitope are arranged in a particular conformation. PSG3 inhibited platelet aggregation induced by either ADP or collagen, it also inhibited fibrinogen binding to activated platelets in a dose-dependent fashion. PSG3, however, did not inhibit the binding of GRGDSP peptide to activated platelets. These results suggest that the PSG3 epitope on GPIIIa contains a particular array of negative charges, and possibly affects the fibrinogen binding to GPIIb/IIIa complex necessary for platelet aggregation.

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