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Quantitative quartz crystal microbalance measurements of the kinetics of the growth of amyloid fibrils in a range of crowded environments have shown the existence of general relationships that have linked the propensities of protein molecules to aggregate with parameters describing their specific structures and local environments.

The effects of naturally occurring [beta]-O-galactosylation of Hyp residues on the conformational stability of the polyproline type II (PPII) helix are examined. Molecular modeling has shown that the increase in conformational stability is due to a regular network of interglycan and glycan-peptide hydrogen bonds, in which the carbohydrate residues have formed a hydrophilic overcoat of the PPII helix.

Turbidity measurements were conducted to provide a detailed description of the binding reaction between islet amyloid polypeptide (IAPP) fibrils and lipid vesicles prepared from phosphatidylcholine. The obtained data and simulation predictions provide insight into the potential roles of IAPP amyloid fibrils in membrane binding.

The reduction of oxidized amyloid fibrils and monomer were compared to understand the link between methionine oxidation and amyloid disease. The results obtained provide insight into the mechanism by which oxidized proteins and aggregates accumulated as a part of degenerative disease.

Short metal-binding NP peptides were efficiently displayed and covalently anchored to the cell wall of Saccharomyces cerevisiae to enhance the biosorption capacity of the potential yeast biosorbent. The results revealed that the biosorption mechanism could be specifically upgraded with microprecipitation by engineering the biosorbent with an eligible metal-binding peptide.

A study was conducted to demonstrate the effect of amino acid polymorphisms on the structural stability and domain cooperativity of gp120 and the differencec reflected in the binding mechanism of the viral envelope glycoprotein to the cell surface receptor and coreceptor. The results for the effects of gp120 polymorphisms on binding to host cell receptors highlights the rules for the future development of entry inhibitors that must recognize and deal with genomic differences between HIV strains.

Standard linear Fmoc/t-Bu solid-phase synthesis of the 42-mer [beta]-amyloid (1-42) peptide is achieved under controlled microwave conditions by using inexpensive DIC/HOBt as coupling reagent on ChemMatrix resin. The racemization of the sensitive amino acids is avoided by performing the coupling of the three His residues in the difficult peptide sequence at room temperature.

The expressed protein ligation method was used to synthesize androgenic gland hormone (AGH) of the woodlouse, Armadillidium vulgare, a heterodimeric glycopeptide, with a homogeneous N-linked glycan. The thermodynamically unstable form of the native conformation of AGH indicated that the correct disulfide linkage is critical for conferring AGH activity.

A study is conducted to assess the ability of various non-natural nucleosides that imitate the core structure of adenosine to modulate drug resistance by inhibiting the ATPase activity to P-glycoprotein (P-gp). The results for the paradoxical behavior of 5-cyclohexylindolyl-2?-deoxyribose (5-CHInd) analogue which rationalized with the context of contemporary models of P-gp function could be applied to develop a predictive in vitro model for rapidly identifying potential drug-drug interactions with P-gp.

The various effects of the wall structure, macromolecular composition and the surface polymers on the survival and hydrologic transport of Cryptosporidium parvum oocysts are determined. The strength of these oocsyt walls is shown to be highly dependent on an inner layer of glycoprotein.

Four [alpha]-synuclein (aS) variants with identical amino acid compositions but rearranged pseudorepeat motifs are used to show that [beta]2-[beta]5 sequence clustering, but not order, is important for efficient fibrillogenesis. The basis of the universal cross-[beta]-sheet structure of amyloid fibrils as useful principle could find application for a wide range of amyloidogenic proteins.

A study of congo red (CR) which interacts with amyloid [beta] peptide (A[beta]) in a pattern similar to that of anionic detergents to reduce the toxicity of A[beta] aggregates in cell cultures and model organisms is presented. CR which promotes [beta] sheet formation and peptide aggregation might also solubilize toxic protein species to make them less harmful to critical cellular components and thereby reduce amyloid toxicity.

Cos-1 cell expression system was employed to demonstrate the ability of activator membrane type 1-matrix metalloproteinase (MT1-MMP) to degrade exogenous [beta]-amyloid (A[beta]40 and A[beta]42). Purified MT1-MMP which degraded parenchymal fibrillar amyloid plaques formed in the brains of A[beta] precursor protein transgenic mice indicated that MT1-MMP possess A[beta] degrading activity in vitro.

Combination of UV difference, near UV circular dichroism, folding kinetics, and multidimensional heteronuclear NMR spectroscopy were used to characterize the conformation of Ribonuclease A (RNase A) in 40% acetic acid and in 8 M urea. The model for RNase A oligomerization revised by 3D domain swapping of its N-terminal [alpha]-helix, C-terminal [beta]-strand, or both could find general implications for amyloid formation.

Several peptides/small proteins and glycosylphosphatidylinositol (GPI) derivatives were prepared in order to compare them as substrates of sortase A (SrtA), a bacterial transpeptidase, for enzymatic coupling. The results suggested that the developed process could be used to synthesize several analogues of the human CD52 and CD24 antigens, which are naturally GPI-anchored glycopeptides/glycoproteins.

A model that postulates formation of an early helical intermediate during amyloid formation where the helical region is localized to the N-terminal region of islet amyloid polypeptide (IAPP) is used to rationalize the inhibition of human IAPP amyloid formation by rat IAPP. The implications of both the point mutants, A13P and F15D of rat IAPP which inhibit amyloid formation by human IAPP and are noticeably less effective inhibitors than wild-type rat IAPP are discussed.

A substructure combination strategy is used for developing potent and selective transthyretin (TTR) kinetic stabilizers that rescue cells from the cytotoxic effects of TTR amyloidogenesis. High-resolution TTR.[(kinetic stabilizer).sub.2] crystal structures have shown the anticipated binding orientation of the 3,5-dibromo-4-hydroxyphenyl substructure and have disclosed a strong preference of the isosteric 3,5-dibromo-4-aminopheyl substructure to bind to the inner thyroxine binding pocket of TTR.

The conformational and physical properties of the disordered C-terminal domain of TAR DNA-binding protein 43 (TDP-43) are clarified by preparing many peptide fragments and showing that only D1 within D1-4 has formed twisted fibrils with a cross section under the incubation of phosphate buffer. The studies have shown that all the three peptides formed an amyloid structure, which has provided insights into the nature of its aggregation with regard to the other fragments in the C-terminus of TDP-43.

Combination of infrared, Raman, and vacuum-ultraviolet circular dichroism spectroscopy were used to study the differences in the molecular structures of [[beta].sub.2]-microglobulin between the two morphologically different amyloid fibrils exhibiting a needlelike [long-straight (LS)] and flexible [wormlike (WL)] character. The site-specific interactions which generally cause variation in the p[K.sub.a] of carboxyl side chains in proteins is assumed to influence the observed enthalpic stabilization in the LS fibril and entropic stabilization in the WL fibril.

The structural features of the human islet amyloid polypeptide (IAPP) monomer are probed by using a combination of ion mobility mass spectrometry (IMS-MS) and all-atom replica exchange molecular dynamics (REMD) simulations. The studies have provided evidence of a significant population of [beta]-hairpin conformers for the IAPP peptide.

The eight-residue alanine oligopeptide Ac-[A.sub.4]K[A.sub.2]Y-N[H.sub.2] (AKY8) has formed amyloid-like fibrils upon incubation at room temperature in acidified aqueous solution at peptide concentrations. The results have provided a pivotal role for the C-terminal tyrosine residue in stabilizing the aggregation state of the peptide and the fibril solution has displayed an increased vibrational circular dichroism couplet in the amide region.

The study evidence for certain [gamma]-secretase modulators (GSMs) that target the 99-residue C-terminal domain (C99) of the amyloid precursor protein, a substrate of [gamma]-secretase, but not the protease complex itself is presented. The results from NMR demonstrated a lack of specific binding for GSMs to monodisperse C99 in LMPG micelles and nonspecific nature of bindings of GSMs to C99 aggregates.

The NMR spectroscopy technique is employed to analyze the various putative amyloidogenic regions present in the SEVI precursor peptide, [PAP.sub.248-286]. The peptide is shown to exhibit a highly disordered structure on being bound to the surface of the micelle.

Several molecular dynamics simulations are conducted to explain the structures of the [beta]-amyloid peptide 1-40, 1-42 and a fragment of amyloid protein precursor (APP) present in a membrane environment. The differences observed in the structures of the protein and its precursor are also discussed.

Series of biophysical methods are employed to study the kinetics and molecular details of PAPf39, a 39-residue peptide fibrillization involved in HIV etiology. The study observations suggested that the nucleation and fibrillization of the PAPf39 peptide are a tug-of-war between the interactions formed upon agitation and the electrostatic interactions, modulated by pH and salt concentration.

Nucleated polymerization mechanism is used to demonstrate the formation of amyloid fibrils from the 8 and 5 kDa human plasma gelsolin fragments which result in domain 2 misfolding within the secretory pathway. The failure of 68 kDa fragment of gelsolin to form amyloid fibrils in vitro proposed a new pathway to administer MT1-MMP inhibitor as an effective strategy for the treatment of familial amyloidosis of finnish type (FAF) disease.

On-pathway oligomers of the 140-residue protein [alpha]-synuclein, a key player in Parkinson's disease, are prepared. The oligomers have formed ion channels with well-defined conductance states in a variety of members and their [beta]-structure has differed from that of amyloid fibrils of [alpha]-synuclein.

The 101-108 fragment of myelin oligodendrocyte glycoprotein (MOG) has played a key role in the interaction with the multiple sclerosis (MS)-autoantibody 8-18C5 and hence the equilibrium conformations of this peptide are analyzed by using the Replica Exchange Molecular Dynamics method in conjunction with the Generalized Born continuum solvent model. The MOG 101-108 fragment has represented a good starting point for designing a drug capable of blocking the 8-18C5 antibody and the molecule can be used for developing a diagnostic assay for MS.

A novel compound library of synthetic polymorphic epithelial mucin (MUC1) glycopeptides has allowed the first rapid and evaluation of the specific epitope structure of anti-Krebs von den Lungen-6 monoclonal antibody (anti-KL-6 MAb) by using a tailored glycopeptides library and common ELISA protocol. The strategy has facilitated the processes for identifying the tumor-specific and strong epitopes and anti-MUC1 MAbs and has allowed their application in the generation of improved antibody immunotherapeutics, diagnosticsand MUC1-based cancer vaccines.

The synthesis of 2,6-sialylated tridecasaccharide associated with the Fc fragment of intravenous immunoglobulin is described.

The construction of a combinatorial artificial receptor array (CARA) and the application of the array to differentiate of proteins based on their binding patterns are described. Four fluorescently labeled proteins, ubiquitin, myoglobin, [alpha]-1-acid glycoprotein and lysozyme, are incubated with the arrays to show the reproducibility of binding and the level of differentiation that can be achieved and the binding environments are stable, scalable, and adaptable to other formats.

The formation of the amyloid fibrils in solutions by the precursors of the human pro-islet amyloid polypeptide (hIAPP) in humans is discussed. The results demonstrate that the hIAPP precursors play a major role in the prevention of aggregation and membrane change of mature hIAPP and hence are extremely significant.

The application of NSAID-like compounds for the preferential inhibition of the [gamma]-secretase cleavage of the amyloid precursor protein (APP) is discussed. The development and screening of selective inhibitors are also discussed.

A combination of the Fourier transform infrared spectroscopy and two-dimensional COS analysis is employed to explain the impact of aggregation propensity and stability on the formation of amyloid fibril. The formation of the fibril is shown to be independent of the aggregation tendency, as well as the stability of each variant.

The impact of the interactions of annexin A5 on the toxicity and other properties of the various amyloidogenic proteins is discussed. The results prove that annexin A5 leads to the reduction of the toxicity of these proteins, hence safeguarding the formation of the toxic amyloid aggregates.

Phototriggering of the metal-free azide to acetylene cycloaddition reaction is achieved by masking the triple bond of dibenzocyclooctynes as cyclopropenone. The cyclopropenone-based phototriggered click chemistry has offered good opportunities to label living organisms in a temporally and spatially controlled manner and has facilitated the preparation of microarrays.

The effect of the changes in the length of the amide-containing side chain between the carbohydrate moiety and the polypeptide backbone in antifreeze glycoprotein (AFGP) analogues on ice recrystallization inhibition (IRI) activity is analyzed. The results have shown how the subtle changes in conformation and carbohydrate orientation have affected IRI activity in C-linked AFGP analogues.

The importance of specific stretches of hydrophobic residues are explored to understand their contribution towards polymerization of [alpha]-synuclein which is the major component of pathological inclusions characteristic of diseases like Parkinson's disease, dementia with Lewy bodies, and multiple-system atrophy. The result obtained provides insight into the significance of both the location and hydrophobicity of protein segments for formation of amyloid fibrils and structural folding of polypeptide into amyloid.

The membrane-induced conformational change of [[alpha].sub.1]-acid glycoprotein (AGP) is studied by measuring the vacuum-ultraviolet circular dichroism (VUVCD) spectra of AGP and its constituent sugars in the presence or absence of phosphoglyceride liposome using a synchrotron-radiation VUVCD spectrophotometer. The studies have provided the first sequence-level information on the membrane-binding mechanism and structure-function relationship of AGP.