The ParB clamp docks onto Smc for DNA loading via a joint-ParB interface

2021 ◽  
Author(s):  
Florian Patrick Bock ◽  
Anna Anchimiuk ◽  
Marie-Laure Diebold-Durand ◽  
Stephan Gruber
Keyword(s):  
Bacillus Subtilis ◽  
Structure Prediction ◽  
Replication Origin ◽  
Functional Module ◽  
Cross Linking ◽  
Chimeric Proteins ◽  
Daughter Cells ◽  
Binding Interface ◽  
Dna Loop ◽  
Chemical Cross Linking

Chromosomes readily unlink from one another and segregate to daughter cells during cell division highlighting a remarkable ability of cells to organize long DNA molecules. SMC complexes mediate chromosome folding by DNA loop extrusion. In most bacteria, SMC complexes start loop extrusion at the ParB/parS partition complex formed near the replication origin. Whether they are recruited by recognizing a specific DNA structure in the partition complex or a protein component is unknown. By replacing genes in Bacillus subtilis with orthologous sequences from Streptococcus pneumoniae, we show that the three subunits of the bacterial Smc complex together with the ParB protein form a functional module that can organize and segregate chromosomes when transplanted into another organism. Using chimeric proteins and chemical cross-linking, we find that ParB binds to the Smc subunit directly. We map a binding interface to the Smc joint and the ParB CTP-binding domain. Structure prediction indicates how the ParB clamp presents DNA to the Smc complex to initiate DNA loop extrusion.

scholarly journals Mapping the Contact Sites of the Escherichia coli Division-Initiating Proteins FtsZ and ZapA by BAMG Cross-Linking and Site-Directed Mutagenesis

2018 ◽  
Vol 19 (10) ◽  
pp. 2928 ◽  
Author(s):  
Winfried Roseboom ◽  
Madhvi Nazir ◽  
Nils Meiresonne ◽  
Tamimount Mohammadi ◽  
Jolanda Verheul ◽  
...  
Keyword(s):  
Site Directed Mutagenesis ◽  
Cross Linking ◽  
Directed Mutagenesis ◽  
Amino Acid Residues ◽  
Binding Interface ◽  
Tetrameric Structure ◽  
Z Ring ◽  
Cross Links ◽  
Chemical Cross Linking

Cell division in bacteria is initiated by the polymerization of FtsZ at midcell in a ring-like structure called the Z-ring. ZapA and other proteins assist Z-ring formation and ZapA binds ZapB, which senses the presence of the nucleoids. The FtsZ–ZapA binding interface was analyzed by chemical cross-linking mass spectrometry (CXMS) under in vitro FtsZ-polymerizing conditions in the presence of GTP. Amino acids residue K42 from ZapA was cross-linked to amino acid residues K51 and K66 from FtsZ, close to the interphase between FtsZ molecules in protofilaments. Five different cross-links confirmed the tetrameric structure of ZapA. A number of FtsZ cross-links suggests that its C-terminal domain of 55 residues, thought to be largely disordered, has a limited freedom to move in space. Site-directed mutagenesis of ZapA reveals an interaction site in the globular head of the protein close to K42. Using the information on the cross-links and the mutants that lost the ability to interact with FtsZ, a model of the FtsZ protofilament–ZapA tetramer complex was obtained by information-driven docking with the HADDOCK2.2 webserver.

scholarly journals Interaction of intramembrane metalloprotease SpoIVFB with substrate Pro-σK

2017 ◽  
Vol 114 (50) ◽  
pp. E10677-E10686 ◽  
Author(s):  
Sabyasachi Halder ◽  
Daniel Parrell ◽  
Douglas Whitten ◽  
Michael Feig ◽  
Lee Kroos
Keyword(s):  
Mass Spectrometry ◽  
Bacillus Subtilis ◽  
Rational Design ◽  
Structural Model ◽  
Cross Linking ◽  
Membrane Domain ◽  
Intramembrane Proteases ◽  
Cbs Domain ◽  
Partial Homology ◽  
Chemical Cross Linking

Intramembrane proteases (IPs) cleave membrane-associated substrates in nearly all organisms and regulate diverse processes. A better understanding of how these enzymes interact with their substrates is necessary for rational design of IP modulators. We show that interaction ofBacillus subtilisIP SpoIVFB with its substrate Pro-σKdepends on particular residues in the interdomain linker of SpoIVFB. The linker plus either the N-terminal membrane domain or the C-terminal cystathione-β-synthase (CBS) domain of SpoIVFB was sufficient for the interaction but not for cleavage of Pro-σK. Chemical cross-linking and mass spectrometry of purified, inactive SpoIVFB–Pro-σKcomplex indicated residues of the two proteins in proximity. A structural model of the complex was built via partial homology and by using constraints based on cross-linking data. In the model, the Proregion of Pro-σKloops into the membrane domain of SpoIVFB, and the rest of Pro-σKinteracts extensively with the linker and the CBS domain of SpoIVFB. The extensive interaction is proposed to allow coordination between ATP binding by the CBS domain and Pro-σKcleavage by the membrane domain.

scholarly journals Integrating cross-linking experiments with ab initio protein-protein docking

2018 ◽  
Author(s):  
Thom Vreven ◽  
Devin K. Schweppe ◽  
Juan D. Chavez ◽  
Chad R. Weisbrod ◽  
Sayaka Shibata ◽  
...  
Keyword(s):  
Experimental Data ◽  
Ab Initio ◽  
Structure Prediction ◽  
Complex Structure ◽  
Protein Docking ◽  
Cross Linking ◽  
Test Cases ◽  
List Type ◽  
Cross Links ◽  
Chemical Cross Linking

ABSTRACTAb initio protein-protein docking algorithms often rely on experimental data to identify the most likely complex structure. We integrated protein-protein docking with the experimental data of chemical cross-linking followed by mass spectrometry. We tested our approach using 12 cases that resulted from an exhaustive search of the Protein Data Bank for protein complexes with cross-links identified in our experiments. We implemented cross-links as constraints based on Euclidean distance or void-volume distance. For most test cases the rank of the top-scoring near-native prediction was improved by at least two fold compared with docking without the cross-link information, and the success rates for the top 5 and top 10 predictions doubled. Our results demonstrate the delicate balance between retaining correct predictions and eliminating false positives. Several test cases had multiple components with distinct interfaces, and we present an approach for assigning cross-links to the interfaces. Employing the symmetry information for these cases further improved the performance of complex structure prediction.HighlightsIncorporating low-resolution cross-linking experimental data in protein-protein docking algorithms improves performance more than two fold.Integration of protein-protein docking with chemical cross-linking reveals information on the configuration of higher order complexes.Symmetry analysis of protein-protein docking results improves the predictions of multimeric complex structures

Statistical Force-Field for Structural Modeling Using Chemical Cross-Linking/mass Spectrometry Distance Constraints

2018 ◽  
Author(s):  
Allan J. R. Ferrari ◽  
Fabio C. Gozzo ◽  
Leandro Martinez
Keyword(s):  
Mass Spectrometry ◽  
Amino Acid ◽  
Force Field ◽  
Protein Structures ◽  
Protein Structure Determination ◽  
Structural Modeling ◽  
Cross Linking ◽  
Amino Acid Residues ◽  
Distance Constraints ◽  
Chemical Cross Linking

<div><p>Chemical cross-linking/Mass Spectrometry (XLMS) is an experimental method to obtain distance constraints between amino acid residues, which can be applied to structural modeling of tertiary and quaternary biomolecular structures. These constraints provide, in principle, only upper limits to the distance between amino acid residues along the surface of the biomolecule. In practice, attempts to use of XLMS constraints for tertiary protein structure determination have not been widely successful. This indicates the need of specifically designed strategies for the representation of these constraints within modeling algorithms. Here, a force-field designed to represent XLMS-derived constraints is proposed. The potential energy functions are obtained by computing, in the database of known protein structures, the probability of satisfaction of a topological cross-linking distance as a function of the Euclidean distance between amino acid residues. The force-field can be easily incorporated into current modeling methods and software. In this work, the force-field was implemented within the Rosetta ab initio relax protocol. We show a significant improvement in the quality of the models obtained relative to current strategies for constraint representation. This force-field contributes to the long-desired goal of obtaining the tertiary structures of proteins using XLMS data. Force-field parameters and usage instructions are freely available at http://m3g.iqm.unicamp.br/topolink/xlff <br></p></div><p></p><p></p>

scholarly journals Structure of cyanobacterial phycobilisome core revealed by structural modeling and chemical cross-linking

2021 ◽  
Vol 7 (2) ◽  
pp. eaba5743
Author(s):  
Haijun Liu ◽  
Mengru M. Zhang ◽  
Daniel A. Weisz ◽  
Ming Cheng ◽  
Himadri B. Pakrasi ◽  
...  
Keyword(s):  
Energy Transfer ◽  
Excitation Energy Transfer ◽  
Energy Coupling ◽  
Regulatory Elements ◽  
Photochemical Activity ◽  
Structural Basis ◽  
Bottom Surface ◽  
Cross Linking ◽  
Orange Carotenoid Protein ◽  
Chemical Cross Linking

In cyanobacteria and red algae, the structural basis dictating efficient excitation energy transfer from the phycobilisome (PBS) antenna complex to the reaction centers remains unclear. The PBS has several peripheral rods and a central core that binds to the thylakoid membrane, allowing energy coupling with photosystem II (PSII) and PSI. Here, we have combined chemical cross-linking mass spectrometry with homology modeling to propose a tricylindrical cyanobacterial PBS core structure. Our model reveals a side-view crossover configuration of the two basal cylinders, consolidating the essential roles of the anchoring domains composed of the ApcE PB loop and ApcD, which facilitate the energy transfer to PSII and PSI, respectively. The uneven bottom surface of the PBS core contrasts with the flat reducing side of PSII. The extra space between two basal cylinders and PSII provides increased accessibility for regulatory elements, e.g., orange carotenoid protein, which are required for modulating photochemical activity.

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