The molecular conformation of proteins is sensitive to the nature of the aqueous environment. In particular, the presence of ions can stabilize or destabilize (denature) protein secondary structure. The underlying mechanisms of these actions are still not fully understood. Here, we combine circular dichroism (CD), single-molecule Förster resonance energy transfer, and atomistic computer simulations to elucidate salt-specific effects on the structure of three peptides with large α-helical propensity. CD indicates a complex ion-specific destabilization of the α-helix that can be rationalized by using a single salt-free computer simulation in combination with the recently introduced scheme of ion-partitioning between nonpolar and polar peptide surfaces. Simulations including salt provide a molecular underpinning of this partitioning concept. Furthermore, our single-molecule Förster resonance energy transfer measurements reveal highly compressed peptide conformations in molar concentrations of NaClO(4) in contrast to strong swelling in the presence of GdmCl. The compacted states observed in the presence of NaClO(4) originate from a tight ion-backbone network that leads to a highly heterogeneous secondary structure distribution and an overall lower α-helical content that would be estimated from CD. Thus, NaClO(4) denatures by inducing a molten globule-like structure that seems completely off-pathway between a fully folded helix and a coil state.
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http://dx.doi.org/10.1016/j.bpj.2012.01.035 | DOI Listing |
Biochem Mol Biol Educ
January 2025
Department of Chemistry and Biochemistry, Miami University, Oxford, Ohio, USA.
We created a novel laboratory experience where undergraduate students explore the techniques used to study protein misfolding, unfolding, and aggregation. Despite the importance of protein misfolding and aggregation diseases, protein unfolding is not typically explored in undergraduate biochemistry laboratory classes. Yeast alcohol dehydrogenase (YADH) is used in the undergraduate biochemistry laboratory course at Miami University as the model system to explore protein overexpression and purification, bioinformatics, and enzyme characterization.
View Article and Find Full Text PDFJ Sci Food Agric
January 2025
College of Food Science and Technology, Bohai University, Jinzhou, China.
Background: Soy protein isolate (SPI) has poor emulsifying ability because of its low molecular flexibility and compact structure, limiting its application in extruded protein-based foods. Extrusion technology has emerged as a promising way to alter the structural properties of proteins. Therefore, the impacts of grape seed proanthocyanidin (GSP) on structural and emulsifying characteristics of SPI in extrusion field were explored in this study.
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January 2025
A.N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 ul. Vavilova, Moscow 119991, Russia.
The hydrolysis of proteins by proteases (proteolysis) plays a significant role in biology and food science. Despite the importance of proteolysis, a universal quantitative model of this phenomenon has not yet been created. This review considers approaches to modeling proteolysis in a batch reactor that take into account differences in the hydrolysis of the individual peptide bonds, as well as the limited accessibility (masking) for the enzymes of some hydrolysis sites in the protein substrate.
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December 2024
School of Food and Health, Beijing Technology and Business University, Beijing 100048, China.
The flavor of dairy products crucially affects consumer purchase preference. Although the flavor and sensory perception of milk can be influenced by heat treatment during processing, the exact mechanism remains unclear. Therefore, this study analyzed the whey protein content and structural changes of milk heated at different time and temperature combinations and evaluated the flavor compounds and sensory characteristics of milk.
View Article and Find Full Text PDFInt J Mol Sci
January 2025
Department of System Biology, Institute of Cytology and Genetics, Novosibirsk 630090, Russia.
Transcription factors (TFs) are the main regulators of eukaryotic gene expression. The cooperative binding of at least two TFs to genomic DNA is a major mechanism of transcription regulation. Massive analysis of the co-occurrence of overrepresented pairs of motifs for different target TFs studied in ChIP-seq experiments can clarify the mechanisms of TF cooperation.
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