Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface

Slutzki, Michal; Reshef, Dan; Barak, Yoav; Haimovitz, Rachel; Rotem‐Bamberger, Shahar; Lamed, Raphael; Bayer, Edward A.; Schueler‐Furman, Ora

doi:10.1074/jbc.m115.651208

Cited by 14 publications

(15 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…While Rosetta predicts that directional hydrogen bonding on Ct Asn37 contributes considerably to the binding affinity (computational prediction for Asn37Ala shows a ΔΔG >0.5 kcal/mol), experimentally Ct Asn37 can be replaced smaller residues Ala/Gly/Cys/Ser with no loss in binding affinity [Fig. (a)] as previously discovered . Ct Asp70 is a rim position that tolerates most substitutions in the deep sequencing experiments except for positively charged amino acids, whereas FoldX predicts strong conservation at that position.…”

Section: Resultsmentioning

confidence: 80%

“…(d) and Supporting Information, Table S2]. In this case, the correlation coefficient for the identity line was 0.48 . However, of 23 point mutants tested from clonal titrations and literature references, 4 variants in the Slutzki et al .…”

Section: Resultsmentioning

confidence: 89%

“…These dual binding modes are thought to be biologically relevant . While several different studies have evaluated sequence determinants to affinity and specificity for Type I dockerin–cohesins, most have evaluated a handful of mutations to residues thought to be most important for binding affinity. Knowledge of the binding activity for every single amino acid mutation for the complex would improve knowledge of binding affinity and improve computational predictions.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from C lostridium thermocellum and C lostridium cellulolyticum using deep sequencing

Kowalsky

Whitehead

2016

Proteins

View full text Add to dashboard Cite

The comprehensive sequence determinants of binding affinity for type I cohesin toward dockerin from Clostridium thermocellum and Clostridium cellulolyticum was evaluated using deep mutational scanning coupled to yeast surface display. We measured the relative binding affinity to dockerin for 2970 and 2778 single point mutants of C. thermocellum and C. cellulolyticum, respectively, representing over 96% of all possible single point mutants. The interface ΔΔG for each variant was reconstructed from sequencing counts and compared with the three independent experimental methods. This reconstruction results in a narrow dynamic range of -0.8-0.5 kcal/mol. The computational software packages FoldX and Rosetta were used to predict mutations that disrupt binding by more than 0.4 kcal/mol. The area under the curve of receiver operator curves was 0.82 for FoldX and 0.77 for Rosetta, showing reasonable agreements between predictions and experimental results. Destabilizing mutations to core and rim positions were predicted with higher accuracy than support positions. This benchmark dataset may be useful for developing new computational prediction tools for the prediction of the mutational effect on binding affinities for protein-protein interactions. Experimental considerations to improve precision and range of the reconstruction method are discussed. Proteins 2016; 84:1914-1928. © 2016 Wiley Periodicals, Inc.

show abstract

Section: Resultsmentioning

confidence: 80%

Section: Resultsmentioning

confidence: 89%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from C lostridium thermocellum and C lostridium cellulolyticum using deep sequencing

Kowalsky

Whitehead

2016

Proteins

View full text Add to dashboard Cite

show abstract

“…For example, Rosetta can be used to estimate the contribution of different residues to the overall binding free energy of a cohesin-dockerin complex and help design a mutant with higher specificity. [128] …”

Section: Coarse Grained and Mesoscale Modeling Of Scaffoldinsmentioning

confidence: 97%

“…Substantial advances have been made in recent years [16,59,60,75,95,98,99,[127][128][129][130] and models that are generallyaccepted (at least in gross features) exist for cellulosome structure and function, but the fine details of the molecular mechanisms are still poorly understood. For example, even appended to a CBM, it is not clear how an endoglucanase would be capable of pulling a single polysaccharide chain out of its crystalline environment and forcing the chain productively into its active site cleft.…”

Section: The Role Of Mechanostability In Nanoscale Functionmentioning

confidence: 99%

Nanoscale Engineering of Designer Cellulosomes

et al. 2016

Self Cite

View full text Add to dashboard Cite

Biocatalysts showcase the upper limit obtainable for high-speed molecular processing and transformation. Efforts to engineer functionality in synthetic nanostructured materials are guided by the increasing knowledge of evolving architectures, which enable controlled molecular motion and precise molecular recognition. The cellulosome is a biological nanomachine, which, as a fundamental component of the plant-digestion machinery from bacterial cells, has a key potential role in the successful development of environmentally-friendly processes to produce biofuels and fine chemicals from the breakdown of biomass waste. Here, the progress toward so-called "designer cellulosomes", which provide an elegant alternative to enzyme cocktails for lignocellulose breakdown, is reviewed. Particular attention is paid to rational design via computational modeling coupled with nanoscale characterization and engineering tools. Remaining challenges and potential routes to industrial application are put forward.

show abstract

FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility

et al. 2017

View full text Add to dashboard Cite

CAPRI rounds 28 and 29 included, for the first time, peptide-receptor targets of three different systems, reflecting increased appreciation of the importance of peptide-protein interactions. The CAPRI rounds allowed us to objectively assess the performance of Rosetta FlexPepDock, one of the first protocols to explicitly include peptide flexibility in docking, accounting for peptide conformational changes upon binding. We discuss here successes and challenges in modeling these targets: we obtain top-performing, high-resolution models of the peptide motif for cases with known binding sites but there is a need for better modeling of flanking regions, as well as better selection criteria, in particular for unknown binding sites. These rounds have also provided us the opportunity to reassess the success criteria, to better reflect the quality of a peptide-protein complex model. Using all models submitted to CAPRI, we analyze the correlation between current classification criteria and the ability to retrieve critical interface features, such as hydrogen bonds and hotspots. We find that loosening the backbone (and ligand) RMSD threshold, together with a restriction on the side chain RMSD measure, allows us to improve the selection of high-accuracy models. We also suggest a new measure to assess interface hydrogen bond recovery, which is not assessed by the current CAPRI criteria. Finally, we find that surprisingly much can be learned from rather inaccurate models about binding hotspots, suggesting that the current status of peptide-protein docking methods, as reflected by the submitted CAPRI models, can already have a significant impact on our understanding of protein interactions. Proteins 2017; 85:445-462. © 2016 Wiley Periodicals, Inc.

show abstract

Crucial Roles of Single Residues in Binding Affinity, Specificity, and Promiscuity in the Cellulosomal Cohesin-Dockerin Interface

Cited by 14 publications

References 65 publications

Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from C lostridium thermocellum and C lostridium cellulolyticum using deep sequencing

Determination of binding affinity upon mutation for type I dockerin–cohesin complexes from C lostridium thermocellum and C lostridium cellulolyticum using deep sequencing

Nanoscale Engineering of Designer Cellulosomes

FlexPepDock lessons from CAPRI peptide–protein rounds and suggested new criteria for assessment of model quality and utility

Contact Info

Product

Resources

About