Buffering capacity is determinant for restoring early α-synuclein aggregation
Biophys Chem. 2022 Jan 13;282:106760. doi: 10.1016/j.bpc.2022.106760. Online ahead of print.ABSTRACTFor disordered proteins, including α-synuclein (Syn), the aggregation of which is implicated in Parkinson's disease, it is known that at mild acidic and at the pI solution conditions the use of either strong or weak electrolytes minimized Syn aggregation. The mechanism is driven by electrostatic forces but remains, however, poorly understood. To address this issue, we used two biological buffers as weak electrolytes, at a low concentration (10 mM) and monitored the aggregation of Syn solutions from pH 7 to pH 2, by mea...
Source: Biophysical Chemistry - January 23, 2022 Category: Chemistry Authors: Marco A Saraiva M Helena Flor êncio Source Type: research

Buffering capacity is determinant for restoring early α-synuclein aggregation
Biophys Chem. 2022 Jan 13;282:106760. doi: 10.1016/j.bpc.2022.106760. Online ahead of print.ABSTRACTFor disordered proteins, including α-synuclein (Syn), the aggregation of which is implicated in Parkinson's disease, it is known that at mild acidic and at the pI solution conditions the use of either strong or weak electrolytes minimized Syn aggregation. The mechanism is driven by electrostatic forces but remains, however, poorly understood. To address this issue, we used two biological buffers as weak electrolytes, at a low concentration (10 mM) and monitored the aggregation of Syn solutions from pH 7 to pH 2, by mea...
Source: Biophysical Chemistry - January 23, 2022 Category: Chemistry Authors: Marco A Saraiva M Helena Flor êncio Source Type: research

Buffering capacity is determinant for restoring early α-synuclein aggregation
Biophys Chem. 2022 Jan 13;282:106760. doi: 10.1016/j.bpc.2022.106760. Online ahead of print.ABSTRACTFor disordered proteins, including α-synuclein (Syn), the aggregation of which is implicated in Parkinson's disease, it is known that at mild acidic and at the pI solution conditions the use of either strong or weak electrolytes minimized Syn aggregation. The mechanism is driven by electrostatic forces but remains, however, poorly understood. To address this issue, we used two biological buffers as weak electrolytes, at a low concentration (10 mM) and monitored the aggregation of Syn solutions from pH 7 to pH 2, by mea...
Source: Biophysical Chemistry - January 23, 2022 Category: Chemistry Authors: Marco A Saraiva M Helena Flor êncio Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

Assessing the DNA structural integrity via selective annihilation of Watson-Crick hydrogen bonds: Insights from molecular dynamics simulations
Biophys Chem. 2022 Jan 6;282:106758. doi: 10.1016/j.bpc.2021.106758. Online ahead of print.ABSTRACTUnderstanding the role of base pairing and stacking displayed by polynucleotide chains interwind together resulting in a double-helical B-DNA type structure is crucial to gaining access to the sophisticated structural arrangement of DNA. Several computational and experimental studies hinted towards the dominance of base pairing over stacking for duplex stability. To find out how significant the individual Watson-Crick hydrogen bonds are in maintaining the double-helical integrity of the DNA, in the present article, we selecti...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Pradeep Pant Leena Aggarwal Source Type: research

Size and/or charge asymmetry effects in coulombic fluids in the presence of external fields: From simple electrolytes to molten salts
Biophys Chem. 2021 Dec 22;282:106747. doi: 10.1016/j.bpc.2021.106747. Online ahead of print.ABSTRACTCharged fluids are ubiquitous in biology and in everyday products such as milk, cosmetics, lubricants, paints, or drugs. The stability and aggregation of charged colloidal solutions are of outstanding relevance in nature and in diverse biomedical applications, including the fabrication of photonic materials and scaffolds for biological assemblies, gene therapy, diagnostics, targeted drug delivery, and molecular labeling. When an electrode or a charged colloidal particle is immersed in a Coulombic fluid, an ionic cloud or ele...
Source: Biophysical Chemistry - January 13, 2022 Category: Chemistry Authors: Guillermo Iv án Guerrero-García Source Type: research

An evidence of pores in phospholipid membrane induced by an antimicrobial peptide NK-2
Biophys Chem. 2022 Jan 5;282:106759. doi: 10.1016/j.bpc.2022.106759. Online ahead of print.ABSTRACTNK-2, a peptide derived from a cationic core region of NK-lysin, has emerged as a promising candidate for new antibiotics. In contrast to classical antibiotics, antimicrobial peptides target bacterial membranes and disintegrate the membrane by forming the transmembrane pores. However, complete understanding of the precise mechanisms of cellular apoptosis and molecular basis of membrane selectivity is still in dispute. In the present study, we have shown that NK-2 forms trans-membrane pores on negatively charged phospholipid m...
Source: Biophysical Chemistry - January 10, 2022 Category: Chemistry Authors: Animesh Halder Sanat Karmakar Source Type: research

An evidence of pores in phospholipid membrane induced by an antimicrobial peptide NK-2
Biophys Chem. 2022 Jan 5;282:106759. doi: 10.1016/j.bpc.2022.106759. Online ahead of print.ABSTRACTNK-2, a peptide derived from a cationic core region of NK-lysin, has emerged as a promising candidate for new antibiotics. In contrast to classical antibiotics, antimicrobial peptides target bacterial membranes and disintegrate the membrane by forming the transmembrane pores. However, complete understanding of the precise mechanisms of cellular apoptosis and molecular basis of membrane selectivity is still in dispute. In the present study, we have shown that NK-2 forms trans-membrane pores on negatively charged phospholipid m...
Source: Biophysical Chemistry - January 10, 2022 Category: Chemistry Authors: Animesh Halder Sanat Karmakar Source Type: research

An evidence of pores in phospholipid membrane induced by an antimicrobial peptide NK-2
Biophys Chem. 2022 Jan 5;282:106759. doi: 10.1016/j.bpc.2022.106759. Online ahead of print.ABSTRACTNK-2, a peptide derived from a cationic core region of NK-lysin, has emerged as a promising candidate for new antibiotics. In contrast to classical antibiotics, antimicrobial peptides target bacterial membranes and disintegrate the membrane by forming the transmembrane pores. However, complete understanding of the precise mechanisms of cellular apoptosis and molecular basis of membrane selectivity is still in dispute. In the present study, we have shown that NK-2 forms trans-membrane pores on negatively charged phospholipid m...
Source: Biophysical Chemistry - January 10, 2022 Category: Chemistry Authors: Animesh Halder Sanat Karmakar Source Type: research

Insights into the binding of morin to human γD-crystallin
Biophys Chem. 2021 Dec 29;282:106750. doi: 10.1016/j.bpc.2021.106750. Online ahead of print.ABSTRACTCrystallin aggregation in the eye lens is one of the leading causes of cataract formation. The increase in the human γD-crystallin (HγDC) aggregation propensity has been associated with the oligomerization of its partially folded and fully unfolded structure. A recent study demonstrated that the binding of flavonoid morin (MOR) to HγDC inhibits the fibrillation of this protein. In this work, we carry out an exhaustive search for the possible binding site of MOR on HγDC by combining an ensemble docking...
Source: Biophysical Chemistry - January 9, 2022 Category: Chemistry Authors: Rodrigo Aguayo-Ortiz Dulce C Guzm án-Ocampo Laura Dominguez Source Type: research

Myopathy-associated G154S mutation causes important changes in the conformational stability, amyloidogenic properties, and chaperone-like activity of human αB-crystallin
Biophys Chem. 2021 Dec 20;282:106744. doi: 10.1016/j.bpc.2021.106744. Online ahead of print.ABSTRACTGlycine to serine substitution at position 154 of human αB-crystallin (αB-Cry) is behind the development of cardiomyopathy and late-onset distal myopathy. The current study was conducted with the aim to investigate the structural and functional features of the G154S mutant αB-Cry using various spectroscopic techniques and microscopic analyses. The secondary and tertiary structures of human αB-Cry were preserved mainly in the presence of G154S mutation, but the mutant protein indicated a reduced chaper...
Source: Biophysical Chemistry - January 4, 2022 Category: Chemistry Authors: Kazem Khoshaman Maryam Ghahramani Mohammad Bagher Shahsavani Ali Akbar Moosavi-Movahedi Boris I Kurganov Reza Yousefi Source Type: research

Myopathy-associated G154S mutation causes important changes in the conformational stability, amyloidogenic properties, and chaperone-like activity of human αB-crystallin
Biophys Chem. 2021 Dec 20;282:106744. doi: 10.1016/j.bpc.2021.106744. Online ahead of print.ABSTRACTGlycine to serine substitution at position 154 of human αB-crystallin (αB-Cry) is behind the development of cardiomyopathy and late-onset distal myopathy. The current study was conducted with the aim to investigate the structural and functional features of the G154S mutant αB-Cry using various spectroscopic techniques and microscopic analyses. The secondary and tertiary structures of human αB-Cry were preserved mainly in the presence of G154S mutation, but the mutant protein indicated a reduced chaper...
Source: Biophysical Chemistry - January 4, 2022 Category: Chemistry Authors: Kazem Khoshaman Maryam Ghahramani Mohammad Bagher Shahsavani Ali Akbar Moosavi-Movahedi Boris I Kurganov Reza Yousefi Source Type: research

A strategy based on gene sequencing and molecular docking for analysis and prediction of bioactive peptides in Shuxuetong injection
Biophys Chem. 2021 Dec 24;282:106749. doi: 10.1016/j.bpc.2021.106749. Online ahead of print.ABSTRACTPeptides are a class of protein fragments with relatively high biological activity and intense specificity, which play crucial role in the treatment of Shuxuetong injection (SXT). However, the extraordinary complexity of Chinese medicinal formulates and the lack of systematic identification methods are primary challenges for study of pharmacodynamic peptides. In addition, infinitesimal peptides contents further hinder the identification and structural characterization of polypeptide by traditional means. In this paper, we de...
Source: Biophysical Chemistry - December 31, 2021 Category: Chemistry Authors: Xinyi Jiao Yanchao Xing Haitao Wang Xin Jin Tingting Zhang Xingru Peng Rui Li Liuyi Liang Rui Liu Lifeng Han Zheng Li Source Type: research

A strategy based on gene sequencing and molecular docking for analysis and prediction of bioactive peptides in Shuxuetong injection
Biophys Chem. 2021 Dec 24;282:106749. doi: 10.1016/j.bpc.2021.106749. Online ahead of print.ABSTRACTPeptides are a class of protein fragments with relatively high biological activity and intense specificity, which play crucial role in the treatment of Shuxuetong injection (SXT). However, the extraordinary complexity of Chinese medicinal formulates and the lack of systematic identification methods are primary challenges for study of pharmacodynamic peptides. In addition, infinitesimal peptides contents further hinder the identification and structural characterization of polypeptide by traditional means. In this paper, we de...
Source: Biophysical Chemistry - December 31, 2021 Category: Chemistry Authors: Xinyi Jiao Yanchao Xing Haitao Wang Xin Jin Tingting Zhang Xingru Peng Rui Li Liuyi Liang Rui Liu Lifeng Han Zheng Li Source Type: research

A strategy based on gene sequencing and molecular docking for analysis and prediction of bioactive peptides in Shuxuetong injection
Biophys Chem. 2021 Dec 24;282:106749. doi: 10.1016/j.bpc.2021.106749. Online ahead of print.ABSTRACTPeptides are a class of protein fragments with relatively high biological activity and intense specificity, which play crucial role in the treatment of Shuxuetong injection (SXT). However, the extraordinary complexity of Chinese medicinal formulates and the lack of systematic identification methods are primary challenges for study of pharmacodynamic peptides. In addition, infinitesimal peptides contents further hinder the identification and structural characterization of polypeptide by traditional means. In this paper, we de...
Source: Biophysical Chemistry - December 31, 2021 Category: Chemistry Authors: Xinyi Jiao Yanchao Xing Haitao Wang Xin Jin Tingting Zhang Xingru Peng Rui Li Liuyi Liang Rui Liu Lifeng Han Zheng Li Source Type: research

Biomimetic design of inhibitors of immune checkpoint LILRB4
Biophys Chem. 2021 Dec 22;282:106746. doi: 10.1016/j.bpc.2021.106746. Online ahead of print.ABSTRACTImmune checkpoint inhibitors have become a hot spot in the treatment of acute myeloid leukemia (AML), the most common acute leukemia (blood cancer) in adults. In the present study, molecular insights into the molecular interactions between an immune checkpoint leukocyte immunoglobulin-like receptor b4 (LILRB4) and its mAb h128-3 was explored using molecular dynamics (MD) simulation for the biomimetic design of peptide inhibitor of LILRB4. Both hydrophobic interaction and electrostatic interaction were found favorable for the...
Source: Biophysical Chemistry - December 28, 2021 Category: Chemistry Authors: Yuanyuan Chao Lin Zhang Source Type: research

Biomimetic design of inhibitors of immune checkpoint LILRB4
Biophys Chem. 2021 Dec 22;282:106746. doi: 10.1016/j.bpc.2021.106746. Online ahead of print.ABSTRACTImmune checkpoint inhibitors have become a hot spot in the treatment of acute myeloid leukemia (AML), the most common acute leukemia (blood cancer) in adults. In the present study, molecular insights into the molecular interactions between an immune checkpoint leukocyte immunoglobulin-like receptor b4 (LILRB4) and its mAb h128-3 was explored using molecular dynamics (MD) simulation for the biomimetic design of peptide inhibitor of LILRB4. Both hydrophobic interaction and electrostatic interaction were found favorable for the...
Source: Biophysical Chemistry - December 28, 2021 Category: Chemistry Authors: Yuanyuan Chao Lin Zhang Source Type: research

Biomimetic design of inhibitors of immune checkpoint LILRB4
Biophys Chem. 2021 Dec 22;282:106746. doi: 10.1016/j.bpc.2021.106746. Online ahead of print.ABSTRACTImmune checkpoint inhibitors have become a hot spot in the treatment of acute myeloid leukemia (AML), the most common acute leukemia (blood cancer) in adults. In the present study, molecular insights into the molecular interactions between an immune checkpoint leukocyte immunoglobulin-like receptor b4 (LILRB4) and its mAb h128-3 was explored using molecular dynamics (MD) simulation for the biomimetic design of peptide inhibitor of LILRB4. Both hydrophobic interaction and electrostatic interaction were found favorable for the...
Source: Biophysical Chemistry - December 28, 2021 Category: Chemistry Authors: Yuanyuan Chao Lin Zhang Source Type: research

The pH dependence of emulsifying properties for glutathione disulfide at oil-water interfaces
Biophys Chem. 2021 Dec 23;282:106748. doi: 10.1016/j.bpc.2021.106748. Online ahead of print.ABSTRACTAlthough peptides were widely used in many fields, their interface behaviors as surfactants have not been explored. The results of the surface tension experiments by an automatic surface tension meter indicate that the stability and emulsifying ability of glutathione disulfide (GSSG) under alkaline conditions were stronger than those under acidic conditions. With encoding the different oxygen and nitrogen atoms in GSSG, as well as the different hydrogen atoms bonded with oxygen and nitrogen atoms. The pH Dependence of the nu...
Source: Biophysical Chemistry - December 27, 2021 Category: Chemistry Authors: Mengfei Liu Hong Mo Qingyu Gao Ling Yuan Source Type: research

The pH dependence of emulsifying properties for glutathione disulfide at oil-water interfaces
Biophys Chem. 2021 Dec 23;282:106748. doi: 10.1016/j.bpc.2021.106748. Online ahead of print.ABSTRACTAlthough peptides were widely used in many fields, their interface behaviors as surfactants have not been explored. The results of the surface tension experiments by an automatic surface tension meter indicate that the stability and emulsifying ability of glutathione disulfide (GSSG) under alkaline conditions were stronger than those under acidic conditions. With encoding the different oxygen and nitrogen atoms in GSSG, as well as the different hydrogen atoms bonded with oxygen and nitrogen atoms. The pH Dependence of the nu...
Source: Biophysical Chemistry - December 27, 2021 Category: Chemistry Authors: Mengfei Liu Hong Mo Qingyu Gao Ling Yuan Source Type: research

A novel assay for the determination of PreScission protease by capillary electrophoresis
Biophys Chem. 2021 Nov 13;281:106696. doi: 10.1016/j.bpc.2021.106696. Online ahead of print.ABSTRACTThe detection of protease activity in the body plays a significant role in the early diagnosis of diseases. However, enzymes inevitably come into contact with various complex biological fluids in the body during the flow, which greatly increases the detection difficulty. Therefore, protease detection in vivo has great challenges. Herein, we report a new assay for detecting protease using capillary electrophoresis inside a capillary with semicircular bends. We first designed a peptide substrate, and then the peptide was self-...
Source: Biophysical Chemistry - December 26, 2021 Category: Chemistry Authors: Shuwen Zhou Pengfei Cui Jingyu Sheng Xueli Zhang Pengju Jiang Xinye Ni Kai Cao Lin Qiu Source Type: research

Engineered Sphingomonas sp. KT-1 PahZ1 monomers efficiently degrade poly(aspartic acid)
Biophys Chem. 2021 Dec 20;281:106745. doi: 10.1016/j.bpc.2021.106745. Online ahead of print.ABSTRACTIn recent years, there has been an effort toward creating and utilizing novel biodegradable polymeric materials. As products become available, it is necessary to concurrently search for novel biodegradation catalysts and further investigate the properties of known biodegradation enzymes. Regarding the latter, we recently reported the crystal structure of a dimeric enzyme, Sphingomonas sp. KT-1 PahZ1, capable of degrading poly(aspartic acid), a green alternative to non-biodegradable polycarboxylates. However, the role of the ...
Source: Biophysical Chemistry - December 25, 2021 Category: Chemistry Authors: Timothy Lamantia Amanda Jansch Justin D Marsee Mitch H Weiland Justin M Miller Source Type: research

Engineered Sphingomonas sp. KT-1 PahZ1 monomers efficiently degrade poly(aspartic acid)
Biophys Chem. 2021 Dec 20;281:106745. doi: 10.1016/j.bpc.2021.106745. Online ahead of print.ABSTRACTIn recent years, there has been an effort toward creating and utilizing novel biodegradable polymeric materials. As products become available, it is necessary to concurrently search for novel biodegradation catalysts and further investigate the properties of known biodegradation enzymes. Regarding the latter, we recently reported the crystal structure of a dimeric enzyme, Sphingomonas sp. KT-1 PahZ1, capable of degrading poly(aspartic acid), a green alternative to non-biodegradable polycarboxylates. However, the role of the ...
Source: Biophysical Chemistry - December 25, 2021 Category: Chemistry Authors: Timothy Lamantia Amanda Jansch Justin D Marsee Mitch H Weiland Justin M Miller Source Type: research

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis
Biophys Chem. 2021 Dec 6;281:106736. doi: 10.1016/j.bpc.2021.106736. Online ahead of print.ABSTRACTCytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neu...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Laxmikant Gadhe Arunima Sakunthala Semanti Mukherjee Nitisha Gahlot Riya Bera Ajay Singh Sawner Pradeep Kadu Samir K Maji Source Type: research

His-tag β-galactosidase supramolecular performance
Biophys Chem. 2021 Dec 10;281:106739. doi: 10.1016/j.bpc.2021.106739. Online ahead of print.ABSTRACTβ-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality ...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Sandra S Flores Pedro D Clop Jos é L Barra Carlos E Argara ña Mar ía A Perillo Ver ónica Nolan Julieta M S ánchez Source Type: research

Structural insights into the activation of blood coagulation factor XI zymogen by thrombin: A computational molecular dynamics study
In this study, we employed a combination of molecular docking and microsecond time-scale molecular dynamics simulations to identify the key regions of interaction between fXI and thrombin. The activating complex between the substrate and enzyme was modeled to represent the initial acylation step of the serine-protease hydrolysis mechanism. The proposed solution structural complex, fIX:fIIa, obtained from 3 microseconds of MD refinement, suggests that the activation of factor XI is mediated by thrombin's anion binding exosite-II interactions with A3 and A4 domains. We predict that the two positively charged arginine residue...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Shenna Shearin Divi Venkateswarlu Source Type: research

Dynamic interaction network involving the conserved intrinsically disordered regions in human eIF5
Biophys Chem. 2021 Dec 10;281:106740. doi: 10.1016/j.bpc.2021.106740. Online ahead of print.ABSTRACTTranslation initiation in eukaryotes requires multiple eukaryotic translation initiation factors (eIFs) and involves continuous remodeling of the ribosomal preinitiation complex (PIC). The GTPase eIF2 brings the initiator Met-tRNAi to the PIC. Upon start codon selection and GTP hydrolysis, promoted by eIF5, eIF2-GDP is released in complex with eIF5. Here, we report that two intrinsically disordered regions (IDRs) in eIF5, the DWEAR motif and the C-terminal tail (CTT) dynamically contact the folded C-terminal domain (CTD) and...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Eleanor Elise Paul Kay Ying Lin Nathan Gamble Amy Wei-Lun Tsai Simon H K Swan Yu Yang Matthew Doran Assen Marintchev Source Type: research

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis
Biophys Chem. 2021 Dec 6;281:106736. doi: 10.1016/j.bpc.2021.106736. Online ahead of print.ABSTRACTCytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neu...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Laxmikant Gadhe Arunima Sakunthala Semanti Mukherjee Nitisha Gahlot Riya Bera Ajay Singh Sawner Pradeep Kadu Samir K Maji Source Type: research

His-tag β-galactosidase supramolecular performance
Biophys Chem. 2021 Dec 10;281:106739. doi: 10.1016/j.bpc.2021.106739. Online ahead of print.ABSTRACTβ-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality ...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Sandra S Flores Pedro D Clop Jos é L Barra Carlos E Argara ña Mar ía A Perillo Ver ónica Nolan Julieta M S ánchez Source Type: research

Structural insights into the activation of blood coagulation factor XI zymogen by thrombin: A computational molecular dynamics study
In this study, we employed a combination of molecular docking and microsecond time-scale molecular dynamics simulations to identify the key regions of interaction between fXI and thrombin. The activating complex between the substrate and enzyme was modeled to represent the initial acylation step of the serine-protease hydrolysis mechanism. The proposed solution structural complex, fIX:fIIa, obtained from 3 microseconds of MD refinement, suggests that the activation of factor XI is mediated by thrombin's anion binding exosite-II interactions with A3 and A4 domains. We predict that the two positively charged arginine residue...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Shenna Shearin Divi Venkateswarlu Source Type: research

Dynamic interaction network involving the conserved intrinsically disordered regions in human eIF5
Biophys Chem. 2021 Dec 10;281:106740. doi: 10.1016/j.bpc.2021.106740. Online ahead of print.ABSTRACTTranslation initiation in eukaryotes requires multiple eukaryotic translation initiation factors (eIFs) and involves continuous remodeling of the ribosomal preinitiation complex (PIC). The GTPase eIF2 brings the initiator Met-tRNAi to the PIC. Upon start codon selection and GTP hydrolysis, promoted by eIF5, eIF2-GDP is released in complex with eIF5. Here, we report that two intrinsically disordered regions (IDRs) in eIF5, the DWEAR motif and the C-terminal tail (CTT) dynamically contact the folded C-terminal domain (CTD) and...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Eleanor Elise Paul Kay Ying Lin Nathan Gamble Amy Wei-Lun Tsai Simon H K Swan Yu Yang Matthew Doran Assen Marintchev Source Type: research

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis
Biophys Chem. 2021 Dec 6;281:106736. doi: 10.1016/j.bpc.2021.106736. Online ahead of print.ABSTRACTCytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neu...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Laxmikant Gadhe Arunima Sakunthala Semanti Mukherjee Nitisha Gahlot Riya Bera Ajay Singh Sawner Pradeep Kadu Samir K Maji Source Type: research

His-tag β-galactosidase supramolecular performance
Biophys Chem. 2021 Dec 10;281:106739. doi: 10.1016/j.bpc.2021.106739. Online ahead of print.ABSTRACTβ-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality ...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Sandra S Flores Pedro D Clop Jos é L Barra Carlos E Argara ña Mar ía A Perillo Ver ónica Nolan Julieta M S ánchez Source Type: research

Structural insights into the activation of blood coagulation factor XI zymogen by thrombin: A computational molecular dynamics study
In this study, we employed a combination of molecular docking and microsecond time-scale molecular dynamics simulations to identify the key regions of interaction between fXI and thrombin. The activating complex between the substrate and enzyme was modeled to represent the initial acylation step of the serine-protease hydrolysis mechanism. The proposed solution structural complex, fIX:fIIa, obtained from 3 microseconds of MD refinement, suggests that the activation of factor XI is mediated by thrombin's anion binding exosite-II interactions with A3 and A4 domains. We predict that the two positively charged arginine residue...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Shenna Shearin Divi Venkateswarlu Source Type: research

Dynamic interaction network involving the conserved intrinsically disordered regions in human eIF5
Biophys Chem. 2021 Dec 10;281:106740. doi: 10.1016/j.bpc.2021.106740. Online ahead of print.ABSTRACTTranslation initiation in eukaryotes requires multiple eukaryotic translation initiation factors (eIFs) and involves continuous remodeling of the ribosomal preinitiation complex (PIC). The GTPase eIF2 brings the initiator Met-tRNAi to the PIC. Upon start codon selection and GTP hydrolysis, promoted by eIF5, eIF2-GDP is released in complex with eIF5. Here, we report that two intrinsically disordered regions (IDRs) in eIF5, the DWEAR motif and the C-terminal tail (CTT) dynamically contact the folded C-terminal domain (CTD) and...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Eleanor Elise Paul Kay Ying Lin Nathan Gamble Amy Wei-Lun Tsai Simon H K Swan Yu Yang Matthew Doran Assen Marintchev Source Type: research

Intermediates of α-synuclein aggregation: Implications in Parkinson's disease pathogenesis
Biophys Chem. 2021 Dec 6;281:106736. doi: 10.1016/j.bpc.2021.106736. Online ahead of print.ABSTRACTCytoplasmic deposition of aberrantly misfolded α-synuclein (α-Syn) is a common feature of synucleinopathies, including Parkinson's disease (PD). However, the precise pathogenic mechanism of α-Syn in synucleinopathies remains elusive. Emerging evidence has suggested that α-Syn may contribute to PD pathogenesis in several ways; wherein the contribution of fibrillar species, for exerting toxicity and disease transmission, cannot be neglected. Further, the oligomeric species could be the most plausible neu...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Laxmikant Gadhe Arunima Sakunthala Semanti Mukherjee Nitisha Gahlot Riya Bera Ajay Singh Sawner Pradeep Kadu Samir K Maji Source Type: research

His-tag β-galactosidase supramolecular performance
Biophys Chem. 2021 Dec 10;281:106739. doi: 10.1016/j.bpc.2021.106739. Online ahead of print.ABSTRACTβ-Galactosidase is an important biotechnological enzyme used in the dairy industry, pharmacology and in molecular biology. In our laboratory we have overexpressed a recombinant β-galactosidase in Escherichia coli (E. coli). This enzyme differs from its native version (β-GalWT) in that 6 histidine residues have been added to the carboxyl terminus in the primary sequence (β-GalHis), which allows its purification by immobilized metal affinity chromatography (IMAC). In this work we compared the functionality ...
Source: Biophysical Chemistry - December 19, 2021 Category: Chemistry Authors: Sandra S Flores Pedro D Clop Jos é L Barra Carlos E Argara ña Mar ía A Perillo Ver ónica Nolan Julieta M S ánchez Source Type: research