In vitro protein digestibility of RuBisCO from alfalfa obtained from different processing histories: Insights from free N-terminal and mass spectrometry study

Ribulose-1,5-bisphosphate-carboxylase/oxygenase (RuBisCO) from alfalfa is a potentially climate-friendly alternative protein with a promising amino acid composition. The balance between yield and purity is a challenge for alternative plant proteins, partly due to the naturally occurring antinutrients. Therefore, measuring the in vitro protein digestibility (IVPD) of RuBisCO with various purity levels is of interest. It was hypothesized that the digestibility of RuBisCO from alfalfa might vary with different processing histories and levels of refinement. To test this hypothesis, RuBisCO from alfalfa with 4 different processing histories were subjected to the INFOGEST IVPD protocol and measurement of free N-terminals and peptidomics. The result showed that the digestibility of RuBisCO was high regardless of the processing history and purity, as demonstrated by 77-99% sequence coverage in the gastric phase. In intestinal phase, increase of free N-terminals and lower sequence coverage (< 10%) indicated that the proteins were hydrolyzed to smaller peptides.

Protocols for All-Atom Reconstruction and High-Resolution Refinement of Protein-Peptide Complex Structures

Structural characterizations of protein-peptide complexes may require further improvements. These may include reconstruction of missing atoms and/or structure optimization leading to higher accuracy models. In this work, we describe a workflow that generates accurate structural models of peptide-protein complexes starting from protein-peptide models in C-alpha representation generated using CABS-dock molecular docking. First, protein-peptide models are reconstructed from their C-alpha traces to all-atom representation using MODELLER. Next, they are refined using Rosetta FlexPepDock. The described workflow allows for reliable all-atom reconstruction of CABS-dock models and their further improvement to high-resolution models.

Investigating Protein-Peptide Interactions Using the Schrödinger Computational Suite

The Schrödinger software suite contains a broad array of computational chemistry and molecular modeling tools that can be used to study the interaction of peptides with proteins. These include molecular docking using Glide and Piper, relative binding free energy predictions with FEP+, conformational searches using MacroModel and Desmond, and structural refinement using Prime and PrimeX. In this review we provide a comprehensive overview of these tools and describe their potential application in the identification and optimization of peptide ligands for proteins.