Search results for "SECONDARY STRUCTURE"

Polymorphism, Metastable Species and Interconversion

2014

Abstract The natively unfolded peptide hormone glucagon forms fibrillar structures with amyloid properties. Here, we summarize past advances in glucagon fibrillation and combine them with recent new unpublished data to provide some more general conclusions on how glucagon fibrillation adapts to different physicochemical conditions such as high temperature, pressure, mechanical and chemical stress. Factors such as peptide concentration, accessible surface area, surface hydration of the glucagon molecular state, contact surface, temperature and ionic strength all contribute to fibrillar structure and stability. In addition to fundamental changes in secondary structure, glucagon fibril morphol…

Probing ensemble polymorphism and single aggregate structural heterogeneity in insulin amyloid self-assembly.

2020

Ensembles of protein aggregates are characterized by a nano- and micro-scale heterogeneity of the species. This diversity translates into a variety of effects that protein aggregates may have in biological systems, both in connection to neurodegenerative diseases and immunogenic risk of protein drug products. Moreover, this naturally occurring variety offers unique opportunities in the field of protein-based biomaterials. In the above-mentioned fields, the isolation and structural analysis of the different amyloid types within the same ensemble remain a priority, still representing a significant experimental challenge. Here we address such complexity in the case of insulin for its relevance…

Interplay between RNA structure and protein evolution in HIV-1.

2010

The genomes of many RNA viruses contain abundant secondary structures that have been shown to be important for understanding the evolution of noncoding regions and synonymous sites. However, the consequences for protein evolution are less well understood. Recently, the secondary structure of the HIV-1 RNA genome has been experimentally determined. Using this information, here we show that RNA structure and proteins do not evolve independently. A negative correlation exists between the extent of base pairing in the genomic RNA and amino acid variability. Relaxed RNA structures may favor the accumulation of genetic variation in proteins and, conversely, sequence changes driven by positive sel…

Rapid evolution of translational control mechanisms in RNA genomes

1997

We have introduced 13 base substitutions into the coat protein gene of RNA bacteriophage MS2. The mutations, which are clustered ahead of the overlapping lysis cistron, do not change the amino acid sequence of the coat protein, but they disrupt a local hairpin, which is needed to control translation of the lysis gene. The mutations decreased the phage titer by four orders of magnitude but, upon passaging, the virus accumulated suppressor mutations that raised the fitness to almost wild-type level. Analysis of the pseudorevertants showed that the disruption of the local hairpin, controlling expression of the lysis gene, had apparently been so complete that its restoration by chance mutations…

2019

Codon composition, GC content and local RNA secondary structures can have a profound effect on gene expression, and mutations affecting these parameters, even though they do not alter the protein sequence, are not neutral in terms of selection. Although evidence exists that, in some cases, selection favours more stable RNA secondary structures, we currently lack a concrete idea of how many genes are affected within a species, and whether this is a universal phenomenon in nature. We searched for signs of structural selection in a global manner, analysing a set of 1 million coding sequences from 73 species representing all domains of life, as well as viruses, by means of our newly developed s…

Exploration of Evolutionary Relations between Protein Structures

2008

We describe a new method for the exploration of evolutionary relations between protein structures.

Raman Spectroscopic Signatures of Echovirus 1 Uncoating

2014

ABSTRACT In recent decades, Raman spectroscopy has entered the biological and medical fields. It enables nondestructive analysis of structural details at the molecular level and has been used to study viruses and their constituents. Here, we used Raman spectroscopy to study echovirus 1 (EV1), a small, nonenveloped human pathogen, in two different uncoating states induced by heat treatments. Raman signals of capsid proteins and RNA genome were observed from the intact virus, the uncoating intermediate, and disrupted virions. Transmission electron microscopy data revealed general structural changes between the studied particles. Compared to spectral characteristics of proteins in the intact v…

Bioconjugates of 1’-Aminoferrocene-1-carboxylic Acid with (S)-3-Amino-2-methylpropanoic Acid and L-Alanine

2010

Formal CH 2 insertion in bioconjugates composed of 1'-aminoferrocene-1-carboxylic acid (Fca) and alanine Boc-Ala-Fca-Ala-OCH 3 gives Fca bioconjugates with the β-amino acid (S)-3-amino-2-methylpropanoic acid (Aib). The novel homologous conjugates of ferrocene were fully characterized by spectroscopic and analytical methods. NMR, CD and IR spectroscopy in concert with DFT calculations suggest that the formal "L-Ala-to-(S)-β-Aib mutations" can exert ferrocene helix inversion due to the different stereogenic carbon atoms of L -Ala and (S)-β-Aib. Furthermore, the mutation (de-)stabilizes the conserved secondary structure with two intramolecular hydrogen bonds, depending on the "mutation site". …

Characterization of two alternative Interleukin(IL)-10 5′UTR mRNA sequences, induced by lipopolysaccharide (LPS) stimulation of peripheral blood mono…

2009

Abstract IL-10 production shows a broad-spectrum of individual response, suggesting a genetic component of approximately 75%. Different polymorphisms located close to, or within the IL-10 gene has been demonstrated to influence its transcription rate whereas the post-transcriptional regulation of IL-10 production has not well elucidated. The main responsible elements at this control level are both the 5′- and 3′-untranslated regions (UTR's) of mRNAs, and as the 3′-UTR regions are mainly involved in the stability and decay rate of mRNAs, the 5′-UTR regions mediate the binding rate of the molecule with ribosomal 40S subunit as a cis-acting element. Herein are report data on the identification…

Self-Ordering Secondary Structure of d- and l-Arginine-Derived Polyamidoamino Acids

2017

This paper reports on synthesis, acid–base properties and pH-dependent structuring in water of d-, l- and d,l-ARGO7, bioinspired polymers obtained by polyaddition of the corresponding arginine stereoisomers with N,N′-methylenebis(acrylamide). The circular dichroism spectra of d- and l-ARGO7 showed a peak at 228 nm and quickly and reversibly responded to pH changes, but were nearly unaffected by temperature, ionic strength, and denaturating agents. Theoretical modeling studies of L-ARGO7 showed that it assumed a folded structure. Intramolecular interactions led to transoid arrangements of the main chain reminiscent of the protein hairpin motif. Torsion angles showed a quite similar distribut…