Identification of determinants of lipid and ion transport in TMEM16/anoctamin proteins through a Bayesian statistical analysis
Biophys Chem. 2024 Feb 1;308:107194. doi: 10.1016/j.bpc.2024.107194. Online ahead of print.ABSTRACTThe TMEM16/Anoctamin protein family (TMEM16x) is composed of members with different functions; some members form Ca2+-activated chloride channels, while others are lipid scramblases or combine the two functions. TMEM16x proteins are typically activated in response to agonist-induced rises of intracellular Ca2+; thus, they couple Ca2+-signalling with cell electrical activity or plasmalemmal lipid homeostasis. The structural domains underlying these functions are not fully defined. We used a Naïve Bayes classifier to gain insi...
Source: Biophysical Chemistry - February 24, 2024 Category: Chemistry Authors: Oscar Moran Paolo Tammaro Source Type: research
Identification of determinants of lipid and ion transport in TMEM16/anoctamin proteins through a Bayesian statistical analysis
Biophys Chem. 2024 Feb 1;308:107194. doi: 10.1016/j.bpc.2024.107194. Online ahead of print.ABSTRACTThe TMEM16/Anoctamin protein family (TMEM16x) is composed of members with different functions; some members form Ca2+-activated chloride channels, while others are lipid scramblases or combine the two functions. TMEM16x proteins are typically activated in response to agonist-induced rises of intracellular Ca2+; thus, they couple Ca2+-signalling with cell electrical activity or plasmalemmal lipid homeostasis. The structural domains underlying these functions are not fully defined. We used a Naïve Bayes classifier to gain insi...
Source: Biophysical Chemistry - February 24, 2024 Category: Chemistry Authors: Oscar Moran Paolo Tammaro Source Type: research
Identification of determinants of lipid and ion transport in TMEM16/anoctamin proteins through a Bayesian statistical analysis
Biophys Chem. 2024 Feb 1;308:107194. doi: 10.1016/j.bpc.2024.107194. Online ahead of print.ABSTRACTThe TMEM16/Anoctamin protein family (TMEM16x) is composed of members with different functions; some members form Ca2+-activated chloride channels, while others are lipid scramblases or combine the two functions. TMEM16x proteins are typically activated in response to agonist-induced rises of intracellular Ca2+; thus, they couple Ca2+-signalling with cell electrical activity or plasmalemmal lipid homeostasis. The structural domains underlying these functions are not fully defined. We used a Naïve Bayes classifier to gain insi...
Source: Biophysical Chemistry - February 24, 2024 Category: Chemistry Authors: Oscar Moran Paolo Tammaro Source Type: research
Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies
Biophys Chem. 2024 Feb 16;308:107203. doi: 10.1016/j.bpc.2024.107203. Online ahead of print.ABSTRACTSpin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circu...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Afnan M Jaufer Adam Bouhadana Amir Kharrazizadeh Mingwei Zhou Coray M Colina Gail E Fanucci Source Type: research
Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation
Biophys Chem. 2024 Feb 15;308:107202. doi: 10.1016/j.bpc.2024.107202. Online ahead of print.ABSTRACTAmyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. ...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Maja Jukovi ć Ivana Ratkaj Daniela Kalafatovic Nicholas J Bradshaw Source Type: research
Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies
Biophys Chem. 2024 Feb 16;308:107203. doi: 10.1016/j.bpc.2024.107203. Online ahead of print.ABSTRACTSpin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circu...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Afnan M Jaufer Adam Bouhadana Amir Kharrazizadeh Mingwei Zhou Coray M Colina Gail E Fanucci Source Type: research
Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation
Biophys Chem. 2024 Feb 15;308:107202. doi: 10.1016/j.bpc.2024.107202. Online ahead of print.ABSTRACTAmyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. ...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Maja Jukovi ć Ivana Ratkaj Daniela Kalafatovic Nicholas J Bradshaw Source Type: research
Designing surface exposed sites on Bacillus subtilis lipase A for spin-labeling and hydration studies
Biophys Chem. 2024 Feb 16;308:107203. doi: 10.1016/j.bpc.2024.107203. Online ahead of print.ABSTRACTSpin-labeling with electron paramagnetic resonance spectroscopy (EPR) is a facile method for interrogating macromolecular flexibility, conformational changes, accessibility, and hydration. Within we present a computationally based approach for the rational selection of reporter sites in Bacillus subtilis lipase A (BSLA) for substitution to cysteine residues with subsequent modification with a spin-label that are expected to not significantly perturb the wild-type structure, dynamics, or enzymatic function. Experimental circu...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Afnan M Jaufer Adam Bouhadana Amir Kharrazizadeh Mingwei Zhou Coray M Colina Gail E Fanucci Source Type: research
Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation
Biophys Chem. 2024 Feb 15;308:107202. doi: 10.1016/j.bpc.2024.107202. Online ahead of print.ABSTRACTAmyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. ...
Source: Biophysical Chemistry - February 21, 2024 Category: Chemistry Authors: Maja Jukovi ć Ivana Ratkaj Daniela Kalafatovic Nicholas J Bradshaw Source Type: research
Different behavior of Ferguson plot between agarose and polyacrylamide gels
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, ...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Yui Tomioka Teruo Akuta Masao Tokunaga Tsutomu Arakawa Source Type: research
On the importance of being amidated: Analysis of the role of the conserved C-terminal amide of amylin in amyloid formation and cytotoxicity
Biophys Chem. 2024 Jan 2;307:107168. doi: 10.1016/j.bpc.2023.107168. Online ahead of print.ABSTRACTThe polypeptide hormone Amylin (also known as islet amyloid polypeptide) plays a role in regulation of glucose metabolism, but forms pancreatic islet amyloid deposits in type 2 diabetes. The process of islet amyloid formation contributes to β-cell dysfunction and the development of the disease. Amylin is produced as a pro-from and undergoes processing prior to secretion. The mature hormone contains an amidated C-terminus. Analysis of an alignment of vertebrate amylin sequences reveals that the processing signal for amidation...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Tangweina Yang Ivan Filippov Lakshan Manathunga Aria Baghai Amandine Mar échal Daniel P Raleigh Alexander Zhyvoloup Source Type: research
Different behavior of Ferguson plot between agarose and polyacrylamide gels
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, ...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Yui Tomioka Teruo Akuta Masao Tokunaga Tsutomu Arakawa Source Type: research
On the importance of being amidated: Analysis of the role of the conserved C-terminal amide of amylin in amyloid formation and cytotoxicity
Biophys Chem. 2024 Jan 2;307:107168. doi: 10.1016/j.bpc.2023.107168. Online ahead of print.ABSTRACTThe polypeptide hormone Amylin (also known as islet amyloid polypeptide) plays a role in regulation of glucose metabolism, but forms pancreatic islet amyloid deposits in type 2 diabetes. The process of islet amyloid formation contributes to β-cell dysfunction and the development of the disease. Amylin is produced as a pro-from and undergoes processing prior to secretion. The mature hormone contains an amidated C-terminus. Analysis of an alignment of vertebrate amylin sequences reveals that the processing signal for amidation...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Tangweina Yang Ivan Filippov Lakshan Manathunga Aria Baghai Amandine Mar échal Daniel P Raleigh Alexander Zhyvoloup Source Type: research
Different behavior of Ferguson plot between agarose and polyacrylamide gels
In this study, we conducted Ferguson plot analyses using both agarose and polyacrylamide gels in native electrophoresis and SDS-PAGE. The results revealed intriguing differences in the behavior of bovine serum albumin (BSA) and other model proteins. Specifically, BSA exhibited Ferguson plot slopes that were dependent on the oligomer size in agarose native gel electrophoresis, while such size-dependent behavior was not observed in native-PAGE or SDS-PAGE. These findings suggest that Ferguson plot analysis is a suitable approach when using agarose gel under the electrophoretic conditions employed in this study. Furthermore, ...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Yui Tomioka Teruo Akuta Masao Tokunaga Tsutomu Arakawa Source Type: research
On the importance of being amidated: Analysis of the role of the conserved C-terminal amide of amylin in amyloid formation and cytotoxicity
Biophys Chem. 2024 Jan 2;307:107168. doi: 10.1016/j.bpc.2023.107168. Online ahead of print.ABSTRACTThe polypeptide hormone Amylin (also known as islet amyloid polypeptide) plays a role in regulation of glucose metabolism, but forms pancreatic islet amyloid deposits in type 2 diabetes. The process of islet amyloid formation contributes to β-cell dysfunction and the development of the disease. Amylin is produced as a pro-from and undergoes processing prior to secretion. The mature hormone contains an amidated C-terminus. Analysis of an alignment of vertebrate amylin sequences reveals that the processing signal for amidation...
Source: Biophysical Chemistry - February 17, 2024 Category: Chemistry Authors: Tangweina Yang Ivan Filippov Lakshan Manathunga Aria Baghai Amandine Mar échal Daniel P Raleigh Alexander Zhyvoloup Source Type: research
