Hydrogen-deuterium exchange measurements are becoming increasingly important in studies of the dynamics protein molecules and, particularly, their folding behavior. Electrospray ionization mass spectrometry (ESI-MS) has been used to obtain distribution masses within a population that had undergone hydrogen solution. This information is complementary from nuclear magnetic resonance spectroscopy (NMR) experiments, which measure average occupancy individual sites over molecules. In experiments...

Abstract A new method is proposed for determining energetically favorable positions and orientations functional groups on the surface of proteins with known three‐dimensional structure. From 1,000 to 5,000 copies a group are randomly placed in site subjected simultaneous energy minimization and/or quenched molecular dynamics. The resulting functionality maps protein receptor site, which can take account its flexibility, be used analysis ligand interactions rational drug design. Application...

The small molecule thioflavin T (ThT) is a defining probe for the identification and mechanistic study of amyloid fiber formation. As such, ThT fundamental to investigations serious diseases such as Alzheimer’s disease, Parkinson type II diabetes. For each different protein undergoes conformational conversion β-sheet rich fiber. fluorescence exhibits an increase in quantum yield upon binding these fibers. Despite its widespread use, structural basis specificity changes photophysical...

Islet amyloid polypeptide (IAPP) contributes to the pathogenesis of type II diabetes by depositing as cytotoxic fibers in endocrine pancreas. Fiber formation occurs with a marked conformational change from an unstructured precursor. Using real-time quantitative kinetic methods, fibrillogenesis was characterized function protein, denaturant, and seed concentration. Several observations are sharp contrast expectations for nucleation-dependent polymerization. First, half-time conversion both de...

The conversion of soluble protein into beta-sheet-rich amyloid fibers is the hallmark a number serious diseases. Precursors for many these systems (e.g., Abeta from Alzheimer's disease) reside in close association with biological membrane. Membrane bilayers are reported to accelerate rate assembly. Furthermore, membrane permeabilization by amyloidogenic peptides can lead toxicity. Given nature mature amyloid, it seemingly paradoxical that precursors either intrinsically alpha-helical or...

A central component of a number degenerative diseases is the deposition protein as amyloid fibers. Self-assembly occurs by nucleation-dependent mechanism that gives rise to characteristic sigmoidal reaction profile. The abruptness this transition variable different proteins with implications both chemical and aggressiveness disease. Because nucleation defined rate-limiting step, we have sought determine nature step for model system derived from islet polypeptide. We show two pathways:...

Rational ligand design is a complex problem that can be divided into three parts: the search for optimal positions and orientations of functional groups in binding site, connection such to form candidate ligands, estimation their constants. Approaches addressing first two parts are described present work. They applied construction peptide ligands site human immunodeficiency virus 1 (HIV-1) proteinase. The primary objective test method by comparison results with MVT-101 structure which...

The protein islet amyloid polypeptide (IAPP) is a glucose metabolism associated hormone cosecreted with insulin by the beta-cells of pancreas. In humans type 2 diabetes, IAPP deposits as fibers. assembly intermediates this process are beta-cell death. Here, we examine rat sequence variant under physiological solution conditions. Rat mechanistically informative for fibrillogenesis, it samples intermediate-like states but does not progress to form amyloid. A central challenge was development...

Poration of bacterial membranes by antimicrobial peptides such as magainin 2 is a significant activity performed innate immune systems. Pore formation soluble forms amyloid proteins islet polypeptide (IAPP) implicated in cell death amyloidoses. Similarities structure and poration these two systems suggest commonality mechanism. Here, we investigate compare the mechanisms which induce membrane leakage through measurement liposome kinetics growth inhibition. For both systems, occurs...

Amyloid fiber formation is correlated with pathology in many diseases, including Alzheimer’s, Parkinson’s, and type II diabetes. Although β-sheet–rich fibrillar protein deposits define this class of disorder, increasing evidence points toward small oligomeric species as being responsible for cell dysfunction death. The molecular mechanism by which occurs unknown, but likely involves the interaction these biological membranes, a subsequent loss integrity. Here, we investigate islet amyloid...

The unfolding and refolding properties of human lysozyme two amyloidogenic variants (Ile56Thr Asp67His) have been studied by stopped-flow fluorescence hydrogen exchange pulse labeling coupled with mass spectrometry. each protein in 5.4 M guanidine hydrochloride (GuHCl) is well described as a two-state process, but the rates Ile56Thr variant Asp67His GuHCl are ca. 30 160 times greater, respectively, than that wild type. all three proteins 0.54 at pH 5.0 proceeds through persistent...

Split personality: A series of oligoamide-based helix mimetics bind to a complementary helical motif in Islet amyloid polypeptide (IAPP), protein implicated the pathology type II diabetes. These compounds accelerated IAPP formation under lipid-free conditions, but inhibited it lipid-catalyzed conditions. hIAPP=human IAPP.

Abstract Disordered proteins, such as those central to Alzheimer’s and Parkinson’s, are particularly intractable for structure-targeted therapeutic design. Here we demonstrate the capacity of a synthetic foldamer capture structure in disease relevant peptide. Oligoquinoline amides have defined fold with solvent-excluded core that is independent its outwardly projected, derivatizable moieties. Islet amyloid polypeptide (IAPP) peptide β-cell pathology type II diabetes. A tetraquinoline...