The Kinetics of Amyloid Fibrillar Aggregation of Uperin 3.5 Is Directed by the Peptide’s Secondary Structure

Biochemistry ◽  
2019 ◽  
Vol 58 (35) ◽  
pp. 3656-3668 ◽  
Author(s):  
Torsten John ◽  
Tiara J. A. Dealey ◽  
Nicholas P. Gray ◽  
Nitin A. Patil ◽  
Mohammed A. Hossain ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Kinetics Of

scholarly journals Investigation by Synchrotron Radiation Circular Dichroism of the Secondary Structure Evolution of Pepsin under Oxidative Environment

Foods ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 998
Author(s):  
Laetitia Théron ◽  
Aline Bonifacie ◽  
Jérémy Delabre ◽  
Thierry Sayd ◽  
Laurent Aubry ◽  
...  
Keyword(s):  
Circular Dichroism ◽  
Synchrotron Radiation ◽  
Secondary Structure ◽  
Proteolytic Activity ◽  
Digestive Enzyme ◽  
Structure Evolution ◽  
Food Protein ◽  
Maldi Tof ◽  
Kinetics Of ◽  
Circular Dichroïsm

Food processing affects the structure and chemical state of proteins. In particular, protein oxidation occurs and may impair protein properties. These chemical reactions initiated during processing can develop during digestion. Indeed, the physicochemical conditions of the stomach (oxygen pressure, low pH) favor oxidation. In that respect, digestive proteases may be affected as well. Yet, very little is known about the link between endogenous oxidation of digestive enzymes, their potential denaturation, and, therefore, food protein digestibility. Thus, the objective of this study is to understand how oxidative chemical processes will impact the pepsin secondary structure and its hydrolytic activity. The folding and unfolding kinetics of pepsin under oxidative conditions was determined using Synchrotron Radiation Circular Dichroism. SRCD gave us the possibility to monitor the rapid kinetics of protein folding and unfolding in real-time, giving highly resolved spectral data. The proteolytic activity of control and oxidized pepsin was investigated by MALDI-TOF mass spectrometry on a meat protein model, the creatine kinase. MALDI-TOF MS allowed a rapid evaluation of the proteolytic activity through peptide fingerprint. This study opens up new perspectives by shifting the digestion paradigm taking into account the gastric digestive enzyme and its substrate.

Effect of Secondary Structure on the Thermodynamics and Kinetics of PNA Hybridization to DNA Hairpins

2001 ◽  
Vol 123 (44) ◽  
pp. 10805-10813 ◽  
Author(s):  
Stuart A. Kushon ◽  
Jason P. Jordan ◽  
Jennifer L. Seifert ◽  
Henrik Nielsen ◽  
Peter E. Nielsen ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Dna Hairpins ◽  
Thermodynamics And Kinetics ◽  
Kinetics Of

scholarly journals Control of Electrochemical and Ferryloxy Formation Kinetics of Cyt P450s in Polyion Films by Heme Iron Spin State and Secondary Structure

2009 ◽  
Vol 131 (44) ◽  
pp. 16215-16224 ◽  
Author(s):  
Sadagopan Krishnan ◽  
Amila Abeykoon ◽  
John B Schenkman ◽  
James F Rusling
Keyword(s):  
Secondary Structure ◽  
Spin State ◽  
Heme Iron ◽  
Formation Kinetics ◽  
Kinetics Of

Nucleation Kinetics of Calcium Phosphates on Polyelectrolyte Multilayers Displaying Internal Secondary Structure

2006 ◽  
Vol 6 (1) ◽  
pp. 327-334 ◽  
Author(s):  
Vincent Ball ◽  
Marc Michel ◽  
Fouzia Boulmedais ◽  
Joseph Hemmerle ◽  
Youssef Haikel ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Calcium Phosphates ◽  
Polyelectrolyte Multilayers ◽  
Nucleation Kinetics ◽  
Kinetics Of

scholarly journals Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure

2021 ◽  
Author(s):  
Sophie Hertel ◽  
Richard Spinney ◽  
Stephanie Xu ◽  
Thomas E Ouldridge ◽  
Richard Morris ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Dna Sequences ◽  
Physical Factors ◽  
Biological Processes ◽  
Physical Mechanisms ◽  
Mechanistic Insight ◽  
Sequence Dependent ◽  
Dna Hybridisation ◽  
Kinetics Of ◽  
Insight Into

The kinetics of DNA hybridisation are fundamental to biological processes and DNA-based technologies. However, the precise physical mechanisms that determine why different DNA sequences hybridise at different rates are not well understood. Secondary structure is one predictable factor that influences hybridisation rates but is not sufficient on its own to fully explain the observed sequence-dependent variance. Consequently, to achieve a good correlation with experimental data, current prediction algorithms require many parameters that provide little mechanistic insight into DNA hybridisation. In this context, we measured hybridisation rates of 43 different DNA sequences that are not predicted to form secondary structure and present a parsimonious physically justified model to quantify their hybridisation rates. Accounting only for the combinatorics of complementary nucleating interactions and their sequence-dependent stability, the model achieves good correlation with experiment with only two free parameters, thus providing new insight into the physical factors underpinning DNA hybridisation rates.

scholarly journals Heat, Cold and Pressure Induced Denaturation of Proteins

2003 ◽  
Vol 17 (2-3) ◽  
pp. 367-376 ◽  
Author(s):  
G. Panick ◽  
H. Herberhold ◽  
Z. Sun ◽  
R. Winter
Keyword(s):  
Infrared Spectroscopy ◽  
Secondary Structure ◽  
Structural Properties ◽  
Relaxation Technique ◽  
Cold Denaturation ◽  
Unfolded State ◽  
Fouriertransform Infrared Spectroscopy ◽  
Monomeric Proteins ◽  
Kinetics Of ◽  
Denaturation Of Proteins

We studied the pressureinduced unfolding and refolding of monomeric proteins, such as SNase, αchymotrypsin and ubiquitin, by using synchrotron Xray smallangle scattering and Fouriertransform infrared spectroscopy, which monitor changes in the tertiary and secondary structural properties of the proteins upon pressurization. Furthermore, by using the pressurejump relaxation technique in combination with timeresolved Xray diffraction and infrared spectroscopy, the kinetics of the unfolding/refolding of the proteins, was investigated. Significant differences in secondary structure and chain compactness in the folding/unfolding reactions of these proteins are observed. The results are compared with data obtained from other methods of denaturation, such as heat and pressure-assisted cold denaturation. The cold- and pressure-induced unfolding both yield a particularly unfolded state characterized by a persistent amount of secondary structure.

RNAKINETICS: A WEB SERVER THAT MODELS SECONDARY STRUCTURE KINETICS OF AN ELONGATING RNA

2006 ◽  
Vol 04 (02) ◽  
pp. 589-596 ◽  
Author(s):  
LUDMILA V. DANILOVA ◽  
DMITRI D. PERVOUCHINE ◽  
ALEXANDER V. FAVOROV ◽  
ANDREI A. MIRONOV
Keyword(s):  
Secondary Structure ◽  
Structure Prediction ◽  
Rna Secondary Structure ◽  
Rna Structures ◽  
Web Interface ◽  
Software Models ◽  
Traditional Structure ◽  
Probabilistic Description ◽  
Folding Pathways ◽  
Kinetics Of

The RNAKinetics server () is a web interface for the newly developed RNAKinetics software. The software models the dynamics of RNA secondary structure by the means of kinetic analysis of folding transitions of a growing RNA molecule. The result of the modeling is a kinetic ensemble, i.e. a collection of RNA structures that are endowed with probabilities, which depend on time. This approach gives comprehensive probabilistic description of RNA folding pathways, revealing important kinetic details that are not captured by the traditional structure prediction methods. The access to the RNAKinetics server is free.

Influence of secondary structure on the decay kinetics of fluorescent donor-acceptor labelled peptides

1997 ◽  
Vol 12 (12) ◽  
pp. 1183-1190 ◽  
Author(s):  
Graham Hungerford ◽  
Fiona Donald ◽  
David J.S. Birch ◽  
Barry D. Moore
Keyword(s):  
Secondary Structure ◽  
Decay Kinetics ◽  
Donor Acceptor ◽  
Kinetics Of

scholarly journals Small Amphipathic Molecules Modulate Secondary Structure and Amyloid Fibril-forming Kinetics of Alzheimer Disease Peptide Aβ1–42

2012 ◽  
Vol 287 (20) ◽  
pp. 16947-16954 ◽  
Author(s):  
Timothy M. Ryan ◽  
Anna Friedhuber ◽  
Monica Lind ◽  
Geoffrey J. Howlett ◽  
Colin Masters ◽  
...  
Keyword(s):  
Secondary Structure ◽  
Alzheimer Disease ◽  
Amyloid Fibril ◽  
Kinetics Of
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