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Zanjani

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See detailKinetic Control of Parallel versus Antiparallel Amyloid Aggregation via Shape of the Growing Aggregate
Hakami Zanjani, Ali Asghar UL; Reynolds, Nicholas; Zhang, Afang et al

in Nature Scientific Reports (2019)

By combining atomistic and higher-level modelling with solution X-ray diffraction we analyse self-assembly pathways for the IFQINS hexapeptide, a bio-relevant amyloid former derived from human lysozyme ... [more ▼]

By combining atomistic and higher-level modelling with solution X-ray diffraction we analyse self-assembly pathways for the IFQINS hexapeptide, a bio-relevant amyloid former derived from human lysozyme. We verify that (at least) two metastable polymorphic structures exist for this system which are substantially different at the atomistic scale, and compare the conditions under which they are kinetically accessible. We further examine the higher-level polymorphism for these systems at the nanometre to micrometre scales, which is manifested in kinetic differences and in shape differences between structures instead of or as well as differences in the small-scale contact topology. Any future design of structure based inhibitors of the IFQINS steric zipper, or of close homologues such as TFQINS which are likely to have similar structures, should take account of this polymorphic assembly. [less ▲]

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See detailThermodynamics and Aggregation Kinetics of Lysozyme-Derived Peptides
Hakami Zanjani, Ali Asghar UL

Doctoral thesis (2019)

When multiple similar protein or peptide chains form non-covalent aggregates, this is termed 'amyloid'. Many serious progressive diseases such as Alzheimer's and Parkinson's are related to undesirable ... [more ▼]

When multiple similar protein or peptide chains form non-covalent aggregates, this is termed 'amyloid'. Many serious progressive diseases such as Alzheimer's and Parkinson's are related to undesirable amyloid aggregation. From a positive perspective, functional amyloids have applications as robust and versatile biomaterials in nature, nanotechnology, and biomedicine. To probe the properties of the amyloid aggregation process in terms of the structure of molecules and the microscopic interactions between them, molecular simulation methods such as molecular dynamics (MD) and Monte Carlo (MC) can be used. These tools are especially valuable to illustrate short length and time scales not easily accessible for systems in solution via current experimental techniques. In this work the thermodynamics and aggregation kinetics of the ILQINS hexapeptide are studied. ILQINS is a biological material derived from hen's egg-white lysozyme. Two ILQINS homologues, IFQINS and TFQINS are compared to ILQINS and some of the complex physics which leads to the increased amyloidogenicity of these species, which is not expected from first-order consideration of amino acid properties, is discussed. The IFQINS hexapeptide is of particular interest as the human homologue of ILQINS. Solution X-ray and X-ray crystallography are compared to simulation, verifying that at least two metastable polymorphic structures exist for this system which are substantially different at the atomistic scale, and illustrating the physics driving kinetic competition between polymorphs. [less ▲]

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See detailCompetition between crystal and fibril formation in molecular mutations of amyloidogenic peptides
Reynolds, Nicholas; Adamcik, Jozef; Berryman, Josh UL et al

in Nature Communications (2017), 8

Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to ... [more ▼]

Amyloidogenic model peptides are invaluable for investigating assembly mechanisms in disease related amyloids and in protein folding. During aggregation, such peptides can undergo bifurcation leading to fibrils or crystals, however the mechanisms of fibril-to-crystal conversion are unclear. We navigate herein the energy landscape of amyloidogenic peptides by studying a homologous series of hexapeptides found in animal, human and disease related proteins. We observe fibril-to-crystal conversion occurring within single aggregates via untwisting of twisted ribbon fibrils possessing saddle-like curvature and cross-sectional aspect ratios approaching unity. Changing sequence, pH or concentration shifts the growth towards larger aspect ratio species assembling into stable helical ribbons possessing mean-curvature. By comparing atomistic calculations of desolvation energies for association of peptides we parameterise a kinetic model, providing a physical explanation of fibril-to-crystal interconversion. These results shed light on the self-assembly of amyloidogenic peptides, suggesting amyloid crystals, not fibrils, represent the ground state of the protein folding energy landscape. [less ▲]

Detailed reference viewed: 128 (9 UL)