Bibliyometrik Yöntemlerle Dünya Üniversitelerinin Değerlendirilmesinde Karşılaşılan Zorluklar

URAP Araştırma Laboratuvarı, 2009 yılında Enformatik Enstitüsü bünyesinde kurulmuş olup yükseköğretim kurumlarını akademik performansları doğrultusunda değerlendirebilmek için bilimsel metodlar geliştirmeyi hedefler

Identification of a penta- and hexapeptide of islet amyloid polypeptide (IAPP) with amyloidogenic and cytotoxic properties.

Pancreatic arnyloid is found in more than 95 % of type II diabetes patients. Pancreatic amyloid is formed by the aggregation of islet amyloid polypeptide (hIAPP or amylin), which is a 37-residue peptide. Because pancreatic amyloid is cytotoxic, it is believed that its formation is directly associated with the development of the disease. We recently showed that hIAPP amyloid formation follows the nucleation-dependent polymerization mechanism and proceeds via a conformational transition of soluble hIAPP into aggregated beta-sheets. Here, we report that the penta- and hexapeptide sequences, hIAPP(23-27) (FGAIL) and hIAPP(22-27) (NFGAIL) of hIAPP are sufficient for the formation of beta-sheet- containing amyloid fibrils. Although these two peptides differ by only one amino acid residue, they aggregate into completely different fibrillar assemblies. hIAPP(23-27) (FGAIL) fibrils self-assemble laterally into unusually broad ribbons, whereas hIAPP(22-27) (NFGAIL) fibrils coil around each other in a typical arnyloid fibril morphology. hIAPP(20-27) (SNNFGAIL) also aggregates into beta-sheet- containing fibrils, whereas no arnyloidogenicity is found for hIAPP(24-27) (GAIL), indicating that hIAPP(23-27) (FGAIL) is the shortest fibrillogenic sequence of hIAPP. Insoluble amyloid formation by the partial hIAPP sequences followed kinetics that were consistent with a nucleation-dependent polymerization mechanism. hIAPP(22-27) (NFGAIL), hIAPP(20-27) (SNNFGAIL), and also the known fibrillogenic sequence, hIAPP(20-29) (SNNFGAILSS) exhibited significantly lower kinetic and thermodynamic solubilities than the pentapeptide hIAPP(23-27) (FGAIL). Fibrils formed by all short peptide sequences and also by hIAPP(20-29) were cytotoxic towards the pancreatic cell line RIN5fm, whereas no cytotoxicity was observed for the soluble form of the peptides, a notion that is consistent with hIAPP cytotoxicity. Our results suggest that a penta- and hexapeptide sequence of an appropriate amino acid composition can be sufficient for beta-sheet and amyloid fibril formation and cytotoxicity and may assist in the rational design of inhibitors of pancreatic amyloid formation or other arnyloidosis-related diseases

Structural Elements Regulating Amyloidogenesis: A Cholinesterase Model System

Polymerization into amyloid fibrils is a crucial step in the pathogenesis of neurodegenerative syndromes. Amyloid assembly is governed by properties of the sequence backbone and specific side-chain interactions, since fibrils from unrelated sequences possess similar structures and morphologies. Therefore, characterization of the structural determinants driving amyloid aggregation is of fundamental importance. We investigated the forces involved in the amyloid assembly of a model peptide derived from the oligomerization domain of acetylcholinesterase (AChE), AChE586-599, through the effect of single point mutations on β-sheet propensity, conformation, fibrilization, surfactant activity, oligomerization and fibril morphology. AChE586-599 was chosen due to its fibrilization tractability and AChE involvement in Alzheimer's disease. The results revealed how specific regions and residues can control AChE586-599 assembly. Hydrophobic and/or aromatic residues were crucial for maintaining a high β-strand propensity, for the conformational transition to β-sheet, and for the first stage of aggregation. We also demonstrated that positively charged side-chains might be involved in electrostatic interactions, which could control the transition to β-sheet, the oligomerization and assembly stability. Further interactions were also found to participate in the assembly. We showed that some residues were important for AChE586-599 surfactant activity and that amyloid assembly might preferentially occur at an air-water interface. Consistently with the experimental observations and assembly models for other amyloid systems, we propose a model for AChE586-599 assembly in which a steric-zipper formed through specific interactions (hydrophobic, electrostatic, cation-π, SH-aromatic, metal chelation and polar-polar) would maintain the β-sheets together. We also propose that the stacking between the strands in the β-sheets along the fiber axis could be stabilized through π-π interactions and metal chelation. The dissection of the specific molecular recognition driving AChE586-599 amyloid assembly has provided further knowledge on such poorly understood and complicated process, which could be applied to protein folding and the targeting of amyloid diseases

Mapping the Conformational Dynamics and Pathways of Spontaneous Steric Zipper Peptide Oligomerization

The process of protein misfolding and self-assembly into various, polymorphic aggregates is associated with a number of important neurodegenerative diseases. Only recently, crystal structures of several short peptides have provided detailed structural insights into -sheet rich aggregates, known as amyloid fibrils. Knowledge about early events of the formation and interconversion of small oligomeric states, an inevitable step in the cascade of peptide self-assembly, however, remains still limited

Cross-ß spine architecture of fibrils formed by the amyloidogenic segment NFGSVQFV of medin from solid-state NMR and X-ray fibre diffraction measurements

Over 30 polypeptides are known to assemble into highly ordered fibrils associated with pathological disorders known collectively as amyloidoses. Structural studies of short model peptides are beginning to reveal trends in the types of molecular interactions that drive aggregation and stabilize the packing of ß-sheet layers within fibrillar assemblies. This work investigates the molecular architecture of fibrils formed by the peptide AMed42-49 representing residues 42-49 of the 50 amino acid polypeptide medin associated with aortic medial amyloid, the most common form of senile localized amyloid. The peptide aggregates within 2 days to form bundles of microcrystalline-like needles displaying a high degree of order. Fibrils were prepared from peptides containing up to 23 13C labels, and the solid-state nuclear magnetic resonance (SSNMR) method rotational resonance (RR) was used to determine constraints on the distances between selective atomic sites within fibrils. The constraints are consistent with unbroken ß-strands hydrogen bonded in a parallel in-register arrangement within ß-sheets. Further RR measurements identify close (>6.5 Å) contacts between residues F43 and V46 and between S45 and V46, which can only occur between ß-sheet layers and which are consistent with two principal models of ß-sheet arrangements. X-ray fiber diffraction from partially aligned fibrils revealed the classical amyloid diffraction pattern, and comparison of patterns calculated from model coordinates with experimental data allowed determination of a consistent molecular model