A litmus test for classifying recognition mechanisms of transiently binding proteins

Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin’s paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks

Best practices for constructing, preparing, and evaluating protein-ligand binding affinity benchmarks

Free energy calculations are rapidly becoming indispensable in structure-enabled drug discovery programs. As new methods, force fields, and implementations are developed, assessing their expected accuracy on real-world systems (benchmarking) becomes critical to provide users with an assessment of the accuracy expected when these methods are applied within their domain of applicability, and developers with a way to assess the expected impact of new methodologies. These assessments require construction of a benchmark - a set of well-prepared, high quality systems with corresponding experimental measurements designed to ensure the resulting calculations provide a realistic assessment of expected performance when these methods are deployed within their domains of applicability. To date, the community has not yet adopted a common standardized benchmark, and existing benchmark reports suffer from a myriad of issues, including poor data quality, limited statistical power, and statistically deficient analyses, all of which can conspire to produce benchmarks that are poorly predictive of real-world performance. Here, we address these issues by presenting guidelines for (1) curating experimental data to develop meaningful benchmark sets, (2) preparing benchmark inputs according to best practices to facilitate widespread adoption, and (3) analysis of the resulting predictions to enable statistically meaningful comparisons among methods and force fields

Efeitos da administração a longo prazo de dietas com diferentes teores de sódio sobre a função renal de ratos hipertensos

A alta ingestão de sódio contribui significativamente para o desenvolvimento da hipertensão e suas complicações. Dentre estas, a doença renal crônica. Entretanto, os mecanismos moleculares responsáveis pelos danos renais e pela renoproteção produzidos por dietas de alto e baixo sal, respectivamente, são pouco compreendidos. Objetivo: Investigar os efeitos a longo prazo de dietas com diferentes teores de cloreto de sódio sobre a função renal de ratos espontaneamente hipertensos (SHR) focando nos mecanismos moleculares envolvidos no manejo renal de albumina e componentes do sistema renina angiotensina renal (SRA). Métodos: ratos SHR machos recém-desmamados (4 semamas) foram alimentados durante 6 meses com dietas diferindo apenas no teor de NaCl: dieta padrão de sal (NS: 0.3 %), dieta de baixo sal (LS: 0.03%) e dieta de alto teor de sal ( HS: 3%). Foram realizadas análises de função e morfologia renal, avaliação da expressão de componentes-chave envolvidos no manejo renal de albumina, incluindo as proteínas da slit membrane (nefrina e podocina) e do aparato endocítico do túbulo proximal (megalina e cubilina). Além disso, a expressão ea atividade dos componentes do RAS (enzima conversora de angiotensina ACE, ACE2, AT1, AT2 e Mas) também foram examinados. Resultados: HS agravou a hipertensão nos ratos SHR, provocou hipertrofia glomerular, diminuição da expressão renal de nefrina e ECA2, levou à perda da integridade morfológica dos processos podais e ao aumento da proteinúria caracterizado pela perda de albumina e proteínas de alto peso molecular. Por outro lado, a hipertensão grave foi atenuada e disfunção renal foi prevenida pela dieta LS, já que, a proteinúria foi muito menor nestes animais quando comparados aos SHR NS. Tais achados foram associados com uma diminuição da razão de proteína e de atividade das enzimas ECA/ECA2 nos rins e aumento da expressão renal de cubilina. Conclusão: Portanto, os resultados sugerem que a dieta a baixa ingestão de sódio atenua a progressão da hipertensão em ratos SHR e preserva a função renal. Os mecanismo que parcialmente podem explicar estes resultados incluem a modulação intra-renal do balanço ECA/ECA2 e o aumento da expressão renal de cubilina. Contudo, a alta ingestão de sódio agrava a lesão renal hipertensiva e reduz a expressão de nefrina, um componente chave slit diaphragm

A litmus test for classifying recognition mechanisms of transiently binding proteins

Partner recognition in protein binding is critical for all biological functions, and yet, delineating its mechanism is challenging, especially when recognition happens within microseconds. We present a theoretical and experimental framework based on straight-forward nuclear magnetic resonance relaxation dispersion measurements to investigate protein binding mechanisms on sub-millisecond timescales, which are beyond the reach of standard rapid-mixing experiments. This framework predicts that conformational selection prevails on ubiquitin’s paradigmatic interaction with an SH3 (Src-homology 3) domain. By contrast, the SH3 domain recognizes ubiquitin in a two-state binding process. Subsequent molecular dynamics simulations and Markov state modeling reveal that the ubiquitin conformation selected for binding exhibits a characteristically extended C-terminus. Our framework is robust and expandable for implementation in other binding scenarios with the potential to show that conformational selection might be the design principle of the hubs in protein interaction networks

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

The process of protein misfolding and self-assembly into various, polymorphic aggregates is associated with a number of important neurodegenerative diseases. Only recently, crystal structures of several short peptides have provided detailed structural insights into -sheet rich aggregates, known as amyloid fibrils. Knowledge about early events of the formation and interconversion of small oligomeric states, an inevitable step in the cascade of peptide self-assembly, however, remains still limited