scholarly journals Substrate binding and specificity of rhomboid intramembrane protease revealed by substrate–peptide complex structures

2014 ◽  
Vol 33 (20) ◽  
pp. 2408-2421 ◽  
Author(s):  
Sebastian Zoll ◽  
Stancho Stanchev ◽  
Jakub Began ◽  
Jan Škerle ◽  
Martin Lepšík ◽  
...  
Keyword(s):  
Substrate Binding ◽  
Complex Structures ◽  
Peptide Complex ◽  
Substrate Peptide

A structural and functional analysis of type III periplasmic and substrate binding proteins: their role in bacterial siderophore and heme transport

2011 ◽  
Vol 392 (1-2) ◽  
Author(s):  
Byron C.H. Chu ◽  
Hans J. Vogel
Keyword(s):  
Binding Proteins ◽  
Substrate Binding ◽  
Transport Systems ◽  
Complex Structures ◽  
Type Iii ◽  
Heme Transport ◽  
Periplasmic Binding Proteins ◽  
Outer Membrane Transporter ◽  
Α Helix ◽  
Carboxy Terminal

AbstractInEscherichia colithe Fhu, Fep and Fec transport systems are involved in the uptake of chelated ferric iron-siderophore complexes, whereas in pathogenic strains heme can also be used as an iron source. An essential step in these pathways is the movement of the ferric-siderophore complex or heme from the outer membrane transporter across the periplasm to the cognate cytoplasmic membrane ATP-dependent transporter. This is accomplished in each case by a dedicated periplasmic binding protein (PBP). Ferric-siderophore binding PBPs belong to the PBP protein superfamily and adopt a bilobal type III structural fold in which the two independently folded amino and carboxy terminal domains are linked together by a single long α-helix of approximately 20 amino acids. Recent structural studies reveal how the PBPs of the Fhu, Fep, Fec and Chu systems are able to bind their corresponding ligands. These complex structures will be discussed and placed in the context of our current understanding of the entire type III family of Gram-negative periplasmic binding proteins and related Gram-positive substrate binding proteins.

scholarly journals Can AlphaFold2 predict protein-peptide complex structures accurately?

2021 ◽  
Author(s):  
Junsu Ko ◽  
Juyong Lee
Keyword(s):  
Structure Prediction ◽  
Good Accuracy ◽  
Higher Order ◽  
Order Structure ◽  
Sequence Information ◽  
Test Cases ◽  
Complex Structures ◽  
Peptide Complex ◽  
Peptide Complexes

In this preprint, we investigated whether AlphaFold2, AF2, can predict protein-peptide complex structures only with sequence information. We modeled the structures of 203 protein-peptide complexes from the PepBDB DB and 183 from the PepSet. The structures were modeling with concatenated sequences of receptors and peptides via poly-glycine linker. We found that for more than half of the test cases, AF2 predicted the bound structures of peptides with good accuracy, C_alpha-RMSD of a peptide < 3.0 angstrom. For about 40% of cases, the peptide structures were modeled with an accuracy of C_alpha-RMSD < 2.0 angstrom. Our benchmark results clearly show that AF2 has a great potential to be applied to various higher-order structure prediction tasks.

Various Metallopheophorbides as Substrates for Chlorophyll Synthetase

1992 ◽  
Vol 47 (3-4) ◽  
pp. 231-238 ◽  
Author(s):  
Michael Helfrich ◽  
Wolfhart Rüdiger
Keyword(s):  
Metal Ions ◽  
Substrate Binding ◽  
Enzyme Reaction ◽  
Complex Structures ◽  
Pheophorbide A ◽  
Planar Structures ◽  
Square Planar ◽  
Chlorophylls A And B ◽  
Competitive Inhibitors ◽  
Enzyme Test

Abstract Pheophorbide a was prepared from a mixture of chlorophylls a and b by differential extraction with HCl and saponification. The insertion of the following metal ions was investigated: Mg, Zn, Co, Cu, Ni. In the enzyme test with chlorophyll synthetase, the metallopheophorbides fall into two categories: the Mg- and Zn-complexes are good substrates, the Co-, Cu- and Ni-complexes are neither substrates nor competitive inhibitors for the enzyme reaction. This corresponds to two categories of complex structures: Mg- and Zn-porphyrins prefer pentacoordinate square-pyramidal structures, Co-, Cu- and Ni-porphyrins prefer tetracoordinate square-planar structures. A model for substrate binding to chlorophyll synthetase is proposed.

scholarly journals Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein–Peptide Complex Structures

2020 ◽  
pp. 273-287 ◽  
Author(s):  
Aleksandra E. Badaczewska-Dawid ◽  
Alisa Khramushin ◽  
Andrzej Kolinski ◽  
Ora Schueler-Furman ◽  
Sebastian Kmiecik
Keyword(s):  
High Resolution ◽  
Complex Structures ◽  
Peptide Complex

scholarly journals The DnaK chaperones from the archaeon Methanosarcina mazei and the bacterium Escherichia coli have different substrate specificities.

2007 ◽  
Vol 54 (3) ◽  
pp. 509-522 ◽  
Author(s):  
Michal A Zmijewski ◽  
Joanna Skórko-Glonek ◽  
Fabio Tanfani ◽  
Bogdan Banecki ◽  
Agnieszka Kotlarz ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Substrate Binding ◽  
Active Form ◽  
Size Exclusion ◽  
Methanosarcina Mazei ◽  
Binding Domains ◽  
Substrate Peptide ◽  
Exclusion Chromatography

Hsp70 (DnaK) is a highly conserved molecular chaperone present in bacteria, eukaryotes, and some archaea. In a previous work we demonstrated that DnaK from the archaeon Methanosarcina mazei (DnaK(Mm)) and the DnaK from the bacterium Escherichia coli (DnaK(Ec)) were functionally similar when assayed in vitro but DnaK(Mm) failed to substitute for DnaK(Ec) in vivo. Searching for the molecular basis of the observed DnaK species specificity we compared substrate binding by DnaK(Mm) and DnaK(Ec). DnaK(Mm) showed a lower affinity for the model peptide (a-CALLQSRLLS) compared to DnaK(Ec). Furthermore, it was unable to negatively regulate the E. coli sigma32 transcription factor level under heat shock conditions and poorly bound purified sigma32, which is a native substrate of DnaK(Ec). These observations taken together indicate differences in substrate specificity of archaeal and bacterial DnaKs. Structural modeling of DnaK(Mm) showed some structural differences in the substrate-binding domains of DnaK(Mm) and DnaK(Ec), which may be responsible, at least partially, for the differences in peptide binding. Size-exclusion chromatography and native gel electrophoresis revealed that DnaK(Mm) was found preferably in high molecular mass oligomeric forms, contrary to DnaK(Ec). Oligomers of DnaK(Mm) could be dissociated in the presence of ATP and a substrate (peptide) but not ADP, which may suggest that monomer is the active form of DnaK(Mm).

Fibronexus-Like Adhesion Sites are Present at the Invasive Zones of Human Epidermoid Carcinomas

1982 ◽  
Vol 40 ◽  
pp. 106-109
Author(s):  
Irwin I. Singer
Keyword(s):  
Cell Cycle ◽  
Serum Concentration ◽  
Substrate Binding ◽  
High Serum ◽  
Adhesion Sites ◽  
Substrate Adhesion ◽  
Focal Contacts ◽  
Adhesion Complex ◽  
Low Serum

Our previous results indicate that two types of fibronectin-cytoskeletal associations may be formed at the fibroblast surface: dorsal matrixbinding fibronexuses generated in high serum (5% FBS) cultures, and ventral substrate-adhering units formed in low serum (0.3% FBS) cultures. The substrate-adhering fibronexus consists of at least vinculin (VN) and actin in its cytoplasmic leg, and fibronectin (FN) as one of its major extracellular components. This substrate-adhesion complex is localized in focal contacts, the sites of closest substratum approach visualized with interference reflection microscopy, which appear to be the major points of cell-tosubstrate adhesion. In fibroblasts, the latter substrate-binding complex is characteristic of cultures that are arrested at the G1 phase of the cell cycle due to the low serum concentration in their medium. These arrested fibroblasts are very well spread, flattened, and immobile.

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