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J Biomol Struct Dyn ; : 1-9, 2020 Jan 06.
Artigo em Inglês | MEDLINE | ID: mdl-31872783


Src homology 3 (SH3) domains are small protein modules involved in the regulation of important cellular pathways such as proliferation and migration, which canonically prefer to recognize and interact with proline-rich peptide ligands with class I or class II motif. Previously, we identified two self-binding peptides (SBPs) in human c-Src tyrosine kinase, of which the first SBP (fSBP) segment (248SKPQTQGLAK257) fulfills intramolecular interaction with the kinase SH3 domain to regulate the kinase function. The segment (and its equivalents in other c-Src family members) does not contain canonical class II motif (PxxQxL versus PxxPx+), but can bind to SH3 domain in a routine class II mode. Existing theories such as non-polyproline-II binding conformation, unusual peptide-binding pocket and extensive use of contacts cannot explain this atypical recognition phenomenon. Here, we performed a systematic investigation of SH3-fSBP binding in different conditions, including the segment in full-length kinase or in isolated state, the kinase in different forms and the fSBP residue mutations, by using microsecond molecular dynamics simulations, conformational clustering analyses and binding energetics calculations. We purposed a new mechanism that the protein context is primarily responsible for the atypical intramolecular SH3-fSBP recognition in c-Src kinase, which can promote the tight packing of segment against domain surface, support the segment polyproline-II (PPII) conformation in unbound state, and avoid unfavorable segment interactions with SH3 charged region by forming a C-terminal t-turn. In addition, the only proline residue Pro250 of fSBP segment is also required for the segment recognition by SH3 domain in c-Src kinase context; lack of Pro250 residue the segment exhibits considerable disorder and cannot maintain in PPII helical conformation, thus largely impairing the domain-segment binding capability. Further binding analysis confirms that the isolated fSBP peptide cannot bind effectively to SH3 domain out of kinase context, whereas its mutant version, i.e. fSBP(Q253P/L255R) peptide, which possesses the canonical class II motif, exhibits an increased affinity to the domain.Communicated by Ramaswamy H. Sarma.

Mol Omics ; 15(4): 280-295, 2019 08 05.
Artigo em Inglês | MEDLINE | ID: mdl-31112188


Many cell signaling pathways are orchestrated by the weak, transient, and reversible protein-protein interactions that are mediated by the binding of a short peptide segment in one protein (parent protein) to a globular domain in another (partner protein), known as peptide-mediated interactions (PMIs). Previous studies normally had an implicit hypothesis that a PMI is functionally equivalent or analogous to the protein-peptide interaction (PTI) involved in the PMI system, while ignoring parent context contribution to the peptide binding. Here, we perform a systematic investigation on the reasonability and applicability of the hypothesis at structural, energetic and dynamic levels. It is revealed that the context impacts PMIs primarily through conformational constraint of the peptide segments, which can (i) reduce the peptide flexibility and disorder in an unbound state, (ii) help the peptide conformational selection to fit the active pocket of partner proteins, and (iii) enhance the peptide packing tightness against the partners. Long, unstructured and/or middle-located peptide segments seem to be more vulnerable to their context than short, structured and/or terminal ones. The context is found to moderately or considerably improve both the binding affinity and specificity of PMIs as compared to their PTI counterparts; with the context support a peptide segment can contribute to ∼30-60% total binding energy of the whole PMI system, whereas the contribution is reduced to ∼5-50% when the context constraint is released. In addition, we also observe that peptide selectivity is largely impaired or even reversed upon stripping of their parent context (global selectivity decreases from 34.2 to 1.7-fold), by examining the crystal structures of full-length Src family kinases in an autoinhibitory state. Instead of the direct interaction and desolvation that are primarily concerned in traditional studies, peptide flexibility and the entropy penalty should also play a crucial role in the context effect on PMIs. Overall, we suggest that the context factor should not be ignored in most cases, particularly those with peptide segments that are long, highly disordered, and/or located at the middle region of their parent proteins.

J Theor Biol ; 469: 25-34, 2019 May 21.
Artigo em Inglês | MEDLINE | ID: mdl-30802465


Self-binding peptide (SBP) represents a novel biomolecular phenomenon spanning between folding and binding. It is a structurally independent, short peptide segment within a monomeric protein and fulfills biological function by dynamically binding to/unbinding from its target domain in the same monomer. Here, four representative SBP systems, including mouse proto-oncogene Vav, human retinoic acid receptor RARγ, fruit fly scaffold module INAD and crypto 14-3-3 protein Cp14b, are investigated systematically by using atomistic molecular dynamics (MD) simulations and post binding energetics analyses. The native bound structure, artificial unbound state and isolated peptide segment of SBP moieties in the four systems were constructed, analyzed and compared in detail. It is revealed that the SBP interaction with their targets is almost a binding phenomenon at single-molecule level, but presence of a polypeptide linker between the SBP and target can promote the binding efficiency since the linker restriction largely increases the probability of SBP-target encounters in a statistical physics point of view. In this respect, unlike classical peptide-mediated interactions where the intrinsically disordered peptides are folded into an ordered structure upon binding to their protein partners (folding-upon-binding), we herein propose SBPs as a new and reversed biological event that is naturally a folding phenomenon but exhibits a typical binding behavior (binding-upon-folding).

Curr Drug Metab ; 20(3): 170-176, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30317994


BACKGROUND: Protein-peptide recognition plays an essential role in the orchestration and regulation of cell signaling networks, which is estimated to be responsible for up to 40% of biological interaction events in the human interactome and has recently been recognized as a new and attractive druggable target for drug development and disease intervention. METHODS: We present a systematic review on the application of machine learning techniques in the quantitative modeling and prediction of protein-peptide binding affinity, particularly focusing on its implications for therapeutic peptide design. We also briefly introduce the physical quantities used to characterize protein-peptide affinity and attempt to extend the content of generalized machine learning methods. RESULTS: Existing issues and future perspective on the statistical modeling and regression prediction of protein- peptide binding affinity are discussed. CONCLUSION: There is still a long way to go before establishment of general, reliable and efficient machine leaningbased protein-peptide affinity predictors.

Aprendizado de Máquina , Peptídeos/metabolismo , Proteínas/metabolismo , Desenho de Drogas , Humanos , Modelos Moleculares , Peptídeos/uso terapêutico , Ligação Proteica