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OPTIMIZATION OF A DESIGNED PROTEINPROTEIN INTERFACE

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The thesis by Colin H. Lipper focuses on the optimization of a designed protein-protein interface, specifically the heterodimerization of two engineered proteins, Monomer A and Monomer B, derived from the β1 domain of streptococcal protein G. The study explores various strategies to enhance binding affinity through computational mutagenesis, including the introduction of charged residues and metal coordination sites. Despite efforts to create a high-affinity heterodimer, the results indicated that while the designed proteins interacted as intended, they exhibited low binding affinity. However, three variants were found to form homo-oligomers in the presence of zinc ions. The research emphasizes the importance of understanding protein interactions for therapeutic applications and suggests further studies to refine these designs.

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What are PPI prediction methods?

PPI PREDICTION METHODS To develop a computational prediction method, one needs a dataset of known interacting protein pairs (a positive set) and a dataset of non-interacting protein pairs (a negative set), because the method needs to maximize its ability to distinguish between positive and negative datasets.

Who won the Nobel Prize for protein folding problem?

The 2024 Nobel Prize in chemistry recognized Demis Hassabis, John Jumper and David Baker for using machine learning to tackle one of biologys biggest challenges: predicting the 3D shape of proteins and designing them from scratch.

What are the methods of PPI detection?

The in silico methods in PPI detection are sequence-based approaches, structure-based approaches, chromosome proximity, gene fusion, in silico 2 hybrid, mirror tree, phylogenetic tree, and gene expression-based approaches.

What are the methods to determine protein binding?

Methods to Determine Plasma Protein Binding Techniques: UV-visible, fluorescence, infrared, NMR, and circular dichroism. Pros: Provides detailed data on binding constants, sites, and structural changes in proteins. Cons: Not ideal for multi-equilibrium systems and requires extensive data analysis.

How do you optimize protein?

Try to include at least 20-30 grams of protein per meal and 10-15 grams of protein in your snacks. Some research suggests that our muscles are only able to utilize 20-30 grams of protein at one time, so its important to spread out our protein intake throughout the day in snacks and meals.

What are the methods of protein detection?

Protein concentration can be measured directly via absorbance at 280 nm in a UV spectrophotometer, or indirectly using colorimetric methods such as BCA or Bradford assays. Protein can even be quantitated using fluorometric methods.

How do you optimize protein digestion?

Try these 5 tips to boost protein absorption Add Enzyme-rich + Fermented Foods. Eat animal proteins earlier in the day. Keep portions In Check. Try digestive bitters Enzymes. Get into Rest Digest

What are the methods to detect protein-protein interactions?

The in vitro methods in PPI detection are tandem affinity purification, affinity chromatography, coimmunoprecipitation, protein arrays, protein fragment complementation, phage display, X-ray crystallography, and NMR spectroscopy. In in vivo techniques, a given procedure is performed on the whole living organism itself.

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