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- https://bio.libretexts.org/Workbench/Biochem_Remix_Acevedo/04%3A_The_Three-Dimensional_Structure_of_Proteins/4.06%3A_Protein_Aggregates_-_Amyloids_Prions_and_Intracellular_GranulesThe Figure \PageIndex8 shows a comparison of the secondary structures of the native conformation of the light chain and those found in the two different fibrillar forms (A and B) of the amyloid ...The Figure \PageIndex8 shows a comparison of the secondary structures of the native conformation of the light chain and those found in the two different fibrillar forms (A and B) of the amyloid fibrils (panel a). The protein found in the plaques, called the PrP sc (the scrapie form of the normal protein) is insoluble in aqueous solution, protease-resistant, and has a high beta sheet content (43%) and lower alpha helix content (30%) than the normal version of the protein PrPc.
- https://bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/04%3A_The_Three-Dimensional_Structure_of_Proteins/4.10%3A_Protein_Aggregates_-_Amyloids_Prions_and_Intracellular_GranulesThis comprehensive biochemistry resource outlines the intricate processes leading to protein aggregation and their implications in diseases. It covers amyloid, prion, and protein aggregation types, th...This comprehensive biochemistry resource outlines the intricate processes leading to protein aggregation and their implications in diseases. It covers amyloid, prion, and protein aggregation types, the mechanisms of amyloid formation, and their connection to neurodegenerative illnesses like Alzheimer's and Parkinson's.
- https://bio.libretexts.org/Workbench/Biochem_Remix_Acevedo/04%3A_The_Three-Dimensional_Structure_of_Proteins/4.05%3A_Protein_Folding_and_Unfolding_(Denaturation)_-_DynamicsWe note that (i) Sec63 interacts with Sec62 involving a cluster of negatively charged amino-acid residues near the C terminus of Sec63 and positively charged cluster in the N-terminal domain of Sec62,...We note that (i) Sec63 interacts with Sec62 involving a cluster of negatively charged amino-acid residues near the C terminus of Sec63 and positively charged cluster in the N-terminal domain of Sec62, (ii) Sec62 interacts with the N-terminal domain of Sec61α via its C-terminal domain, (iii) BiP can bind to ER luminal loop 7 of Sec61 α via its substrate-binding domain and mediated by the ATPase domain of BiP and the J-domain in the ER luminal loop of Sec63, (iv) Ca 2 + -CaM can bind to an IQ mot…
- https://bio.libretexts.org/Courses/Wheaton_College_Massachusetts/Principles_of_Biochemistry/04%3A_Protein_structure_and_function/4.04%3A_Protein_foldingTo think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomi...To think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomitantly how to probe protein folding experimentally. View the following two MD simulations and compare the spontaenously formation of a micelle and the folding of a protein before we delve into the complex topic of protein folding and stability.
- https://bio.libretexts.org/Courses/Roosevelt_University/BCHM_355_455_Biochemistry_(Roosevelt_University)/04%3A_Proteins-_Structure_and_Folding/4.07%3A_The_Three-Dimensional_Structure_of_Proteins/4.7.10%3A_Protein_Aggregates_-_Amyloids_Prions_and_Intracellular_GranulesThe backbone of the C-terminal amino acid (367-380) of each of the three separate chains of the fibril is shown in CPK colors, and hydrogen bonds between the strands that form the parallel beta strand...The backbone of the C-terminal amino acid (367-380) of each of the three separate chains of the fibril is shown in CPK colors, and hydrogen bonds between the strands that form the parallel beta strands are shown as green dashes. The protein found in the plaques, called the PrP sc (the scrapie form of the normal protein) is insoluble in aqueous solution, protease-resistant, and has a high beta sheet content (43%) and lower alpha helix content (30%) than the normal version of the protein PrPc.
- https://bio.libretexts.org/Courses/Roosevelt_University/BCHM_355_455_Biochemistry_(Roosevelt_University)/04%3A_Proteins-_Structure_and_Folding/4.07%3A_The_Three-Dimensional_Structure_of_Proteins/4.7.08%3A_Protein_Folding_and_Unfolding_(Denaturation)_-_DynamicsWe note that (i) Sec63 interacts with Sec62 involving a cluster of negatively charged amino-acid residues near the C terminus of Sec63 and positively charged cluster in the N-terminal domain of Sec62,...We note that (i) Sec63 interacts with Sec62 involving a cluster of negatively charged amino-acid residues near the C terminus of Sec63 and positively charged cluster in the N-terminal domain of Sec62, (ii) Sec62 interacts with the N-terminal domain of Sec61α via its C-terminal domain, (iii) BiP can bind to ER luminal loop 7 of Sec61 α via its substrate-binding domain and mediated by the ATPase domain of BiP and the J-domain in the ER luminal loop of Sec63, (iv) Ca 2 + -CaM can bind to an IQ mot…
- https://bio.libretexts.org/Courses/Roosevelt_University/BCHM_355_455_Biochemistry_(Roosevelt_University)/04%3A_Proteins-_Structure_and_Folding/4.04%3A_Protein_foldingTo think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomi...To think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomitantly how to probe protein folding experimentally. View the following two MD simulations and compare the spontaenously formation of a micelle and the folding of a protein before we delve into the complex topic of protein folding and stability.
- https://bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/04%3A_The_Three-Dimensional_Structure_of_Proteins/4.08%3A_Protein_Folding_and_Unfolding_(Denaturation)_-_DynamicsThis page provides a comprehensive overview of protein folding, detailing the processes involved, such as thermodynamics driving Gibbs free energy changes, kinetics of folding pathways, and the transi...This page provides a comprehensive overview of protein folding, detailing the processes involved, such as thermodynamics driving Gibbs free energy changes, kinetics of folding pathways, and the transition between native, intermediate, and denatured states. It discusses factors influencing protein denaturation, including temperature and chemical denaturants, and the role of molecular chaperones in assisting folding.
- https://bio.libretexts.org/Bookshelves/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/04%3A_The_Three-Dimensional_Structure_of_Proteins/4.09%3A_Protein_Stability_-_ThermodynamicsThe page delves into protein stability, discussing the balance between folding and unfolding dynamics influenced by thermodynamic factors. Key forces like hydrogen bonds, ion pairs, van der Waals forc...The page delves into protein stability, discussing the balance between folding and unfolding dynamics influenced by thermodynamic factors. Key forces like hydrogen bonds, ion pairs, van der Waals forces, and the hydrophobic effect affect protein stability. It highlights experimental approaches, such as site-directed mutagenesis, to study these forces. Environmental factors, such as pH and temperature, also influence protein behavior.
- https://bio.libretexts.org/Courses/Ouachita_Baptist_University/Reyna_Cell_Biology/02%3A_2-(T2-first_lecture)_Protein_Structure/2.04%3A_Protein_Folding_-_in_Vivo_and_in_Vitro/2.4.01%3A_D1._IntroductionTo think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomi...To think about how proteins fold, we have to think dynamically. Luckily we have the tools of molecular dynamics (MD) at our fingertips which helps us imagine how these processes take place and concomitantly how to probe protein folding experimentally. View the following two MD simulations and compare the spontaenously formation of a micelle and the folding of a protein before we delve into the complex topic of protein folding and stability.
- https://bio.libretexts.org/Courses/Roosevelt_University/BCHM_355_455_Biochemistry_(Roosevelt_University)/04%3A_Proteins-_Structure_and_Folding/4.07%3A_The_Three-Dimensional_Structure_of_Proteins/4.7.09%3A_Protein_Stability_-_ThermodynamicsHence, these alternative sources of explanation for the mutant's destabilization can't account for the data, so we're left with the explanation that the stability of the native protein over the mutant...Hence, these alternative sources of explanation for the mutant's destabilization can't account for the data, so we're left with the explanation that the stability of the native protein over the mutant is accounted for by burying the H bond donor and acceptors of the amide group and associated changes in van der Waals interactions.
