Combinatorial and Computational Approaches to Identify Interactions of Macrophage Colony-stimulating Factor (M-CSF) and Its Receptor c-FMS

Abstract

Background: Identifying residues crucial for M-CSF⅐c-FMS binding remains difficult. Results: Using a combination of experimental and computational methods, we identified mutations on M-CSF that reduce affinity to c-FMS. Conclusion: Affinity-reducing mutations are located both inside and outside of the binding interface. Significance: Knowledge of the critical residues will facilitate a better understanding of the M-CSF mechanism and facilitate drug design.

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

“…Orders of magnitude more data can be generated by experiments measuring the relative binding affinities of entire populations using techniques such as phage display or yeast surface display . In recent years, the ability to deep sequence an entire population has enabled such experiments to be performed routinely . The principle behind these deep mutational scanning experiments is simple: a protein library of mutational variants is passed through a selection or screen for binding affinity.…”

“…10,11 In recent years, the ability to deep sequence an entire population has enabled such experiments to be performed routinely. [12][13][14][15][16] The principle behind these deep mutational scanning experiments is simple: a protein library of mutational variants is passed through a selection or screen for binding affinity. The entire population is sequenced after the selection and compared with a reference population.…”

Asperpyrone A attenuates RANKL‐induced osteoclast formation through inhibiting NFATc1, Ca2+ signalling and oxidative stress

“…Two key cytokines involved in the process of osteoclastogenesis: (a) RANKL (receptor activator of NF‐κB ligand) is an essential cytokine in the process of the osteoclast differentiation, which interacts with RANK to regulate signalling pathways such as NF‐κB, MAPKs and calcium signalling in osteoclasts and then consequently stimulates the downstream factor‐related osteoclastogenesis such as NFATc1 (nuclear factor of activated T cells, cytoplasmic 1) and c‐Fos (a protein of AP‐1 transcription factor required) . (b) M‐CSF (macrophage colony‐stimulating factor) is another crucial cytokine involved in the proliferation and differentiation of monocytes/macrophages, especially in the regulation of the survival and proliferation of pre‐osteoclasts and mature osteoclasts . Additionally, M‐CSF also up‐regulates RANK levels in BMMs (bone marrow macrophage cells) and then enhances the effects of RANKL stimulation on osteoclast differentiation …”

“…7 (b) M-CSF (macrophage colonystimulating factor) is another crucial cytokine involved in the proliferation and differentiation of monocytes/macrophages, especially in the regulation of the survival and proliferation of pre-osteoclasts and mature osteoclasts. 8 Additionally, M-CSF also up-regulates RANK levels in BMMs (bone marrow macrophage cells) and then enhances the effects of RANKL stimulation on osteoclast differentiation. 9 The natural compound of Asperpyrone A was isolated from Aspergillus niger.…”

Residue‐level determinants of angiopoietin‐2 interactions with its receptor Tie2

“…[21][22][23][24][25][26][27][28][29][30] Here, we used two different physics-based computational methodologies to interrogate the high-resolution (residue level) determinants of Ang2-BD binding to Tie2-both directly and indirectly, as defined above. We combined our computational predictions with random and site-directed mutagenesis and yeast surface display (YSD), an orthogonal method that has been used for the in vitro evolution of various proteins, [31][32][33] which identified specific substitutions in Ang2-BD that actually perturbed binding. This combination also provided insights into the use of high-throughput mutagenesis to interrogate the residue-level determinants of Ang2-Tie2 interactions.…”