Effects of Intramolecular Distance between Amyloidogenic Domains on Amyloid Aggregation

Abstract

Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation.

Distribution and Structure Analysis of Fibril-Forming Peptides Focusing on Concentration Dependency

“…The peptide is the KFFE fragment, which consists of only four amino-acid residues, which has been known as a minimum-size fibril-forming peptide . The dimerization mechanism for some kinds of tetrapeptides including the KFFE fragment has been studied by molecular simulations. − The simulation method that we employed is replica-exchange molecular dynamics (REMD), which is one of the efficient conformational sampling techniques. In order to perform simulations at different concentrations, we simply prepared simulation boxes of several different sizes and the same number of fragments (= 30), in other words, the different number density of fragments (see Figure ).…”

One-step isothermal detection of multiple KRAS mutations by forming SNP specific hairpins on a gold nanoshell

“…Several analytical methods for the use of SNPs as the biomarkers have appeared on the market. [8][9][10] Most of the available methods, with a few exceptions, rely on PCR to amplify the target genes so that they can be detected. 11 Basically, the methods involve first generating all of the specific products, either during or after PCR, and then quantifying them by any of several methods, including MALDI-TOF MS, gel electrophoresis, fluorescence detection and sequencing.…”