Intrinsically Disordered Proteins: Phase Separation and Membrane Interactions

This lecture explores the behavior of intrinsically disordered proteins (IDPs), which are common in the human proteome. It covers the characteristics of IDPs, their role in disease, and their transformation into rigid fibrils. The lecture delves into the counter-intuitive problem of polymer phase separation in solutions with weakly hydrophobic polymers. It discusses the Flory-Huggins theory of polymer mixtures, phase transitions, and the entropic spring model. The lecture also examines the equivalence between Flory-Huggins theory and dissipative particle dynamics (DPD) simulations. Additionally, it investigates the formation of biomolecular condensates and membrane interactions, shedding light on the potential of IDPs to create membrane domains.

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Protein structure

Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.

Protein tertiary structure

Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.

Protein quaternary structure

Protein quaternary structure is the fourth (and highest) classification level of protein structure. Protein quaternary structure refers to the structure of proteins which are themselves composed of two or more smaller protein chains (also referred to as subunits). Protein quaternary structure describes the number and arrangement of multiple folded protein subunits in a multi-subunit complex. It includes organizations from simple dimers to large homooligomers and complexes with defined or variable numbers of subunits.

Protein secondary structure

Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.

Protein primary structure

Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthesis is most commonly performed by ribosomes in cells. Peptides can also be synthesized in the laboratory. Protein primary structures can be directly sequenced, or inferred from DNA sequencess.

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Explores protein folding, hydrophobic interactions, compact conformations, the HP model, co-evolution, and computational methods.