Choosing the right density for a concentrated protein system like gluten in a coarse-grained model
Eur Biophys J. 2023 Jun 28. doi: 10.1007/s00249-023-01667-8. Online ahead of print.ABSTRACTLarge coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a w...
Source: European Biophysics Journal : EBJ - June 28, 2023 Category: Physics Authors: Łukasz Mioduszewski Source Type: research
Choosing the right density for a concentrated protein system like gluten in a coarse-grained model
Eur Biophys J. 2023 Jun 28. doi: 10.1007/s00249-023-01667-8. Online ahead of print.ABSTRACTLarge coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a w...
Source: European Biophysics Journal : EBJ - June 28, 2023 Category: Physics Authors: Łukasz Mioduszewski Source Type: research
Choosing the right density for a concentrated protein system like gluten in a coarse-grained model
Eur Biophys J. 2023 Jun 28. doi: 10.1007/s00249-023-01667-8. Online ahead of print.ABSTRACTLarge coarse-grained simulations are often conducted with an implicit solvent, which makes it hard to assess the water content of the sample and the effective concentration of the system. Here the number and the size of cavities and entanglements in the system, together with density profiles, are used to asses the homogeneity and interconnectedness of gluten. This is a continuation of an earlier article, "Viscoelastic properties of wheat gluten in a molecular dynamics study" (Mioduszewski and Cieplak 2021b). It turns out there is a w...
Source: European Biophysics Journal : EBJ - June 28, 2023 Category: Physics Authors: Łukasz Mioduszewski Source Type: research
Twist-stretch relations in nucleic acids
Eur Biophys J. 2023 Jun 25. doi: 10.1007/s00249-023-01669-6. Online ahead of print.ABSTRACTNucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the ...
Source: European Biophysics Journal : EBJ - June 25, 2023 Category: Physics Authors: Marco Zoli Source Type: research
Twist-stretch relations in nucleic acids
Eur Biophys J. 2023 Jun 25. doi: 10.1007/s00249-023-01669-6. Online ahead of print.ABSTRACTNucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the ...
Source: European Biophysics Journal : EBJ - June 25, 2023 Category: Physics Authors: Marco Zoli Source Type: research
Twist-stretch relations in nucleic acids
Eur Biophys J. 2023 Jun 25. doi: 10.1007/s00249-023-01669-6. Online ahead of print.ABSTRACTNucleic acids are highly deformable helical molecules constantly stretched, twisted and bent in their biological functioning. Single molecule experiments have shown that double stranded (ds)-RNA and standard ds-DNA have opposite twist-stretch patterns and stretching properties when overwound under a constant applied load. The key structural features of the A-form RNA and B-form DNA helices are here incorporated in a three-dimensional mesoscopic Hamiltonian model which accounts for the radial, bending and twisting fluctuations of the ...
Source: European Biophysics Journal : EBJ - June 25, 2023 Category: Physics Authors: Marco Zoli Source Type: research
Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Eur Biophys J. 2023 Jun 8:1-8. doi: 10.1007/s00249-023-01663-y. Online ahead of print.ABSTRACTLipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calcul...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Alexander Bepperling Gesa Richter Source Type: research
A model for ribosome translocation based on the alternated displacement of its subunits
Eur Biophys J. 2023 Apr;52(3):175-187. doi: 10.1007/s00249-023-01662-z. Epub 2023 Jun 9.ABSTRACTA meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Jos é S González-García Source Type: research
Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Eur Biophys J. 2023 Jun 8:1-8. doi: 10.1007/s00249-023-01663-y. Online ahead of print.ABSTRACTLipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calcul...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Alexander Bepperling Gesa Richter Source Type: research
A model for ribosome translocation based on the alternated displacement of its subunits
Eur Biophys J. 2023 Apr;52(3):175-187. doi: 10.1007/s00249-023-01662-z. Epub 2023 Jun 9.ABSTRACTA meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Jos é S González-García Source Type: research
Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Eur Biophys J. 2023 Jun 8:1-8. doi: 10.1007/s00249-023-01663-y. Online ahead of print.ABSTRACTLipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calcul...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Alexander Bepperling Gesa Richter Source Type: research
A model for ribosome translocation based on the alternated displacement of its subunits
Eur Biophys J. 2023 Apr;52(3):175-187. doi: 10.1007/s00249-023-01662-z. Epub 2023 Jun 9.ABSTRACTA meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Jos é S González-García Source Type: research
Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Eur Biophys J. 2023 Jun 8:1-8. doi: 10.1007/s00249-023-01663-y. Online ahead of print.ABSTRACTLipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calcul...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Alexander Bepperling Gesa Richter Source Type: research
A model for ribosome translocation based on the alternated displacement of its subunits
Eur Biophys J. 2023 Apr;52(3):175-187. doi: 10.1007/s00249-023-01662-z. Epub 2023 Jun 9.ABSTRACTA meaningful dilemma in ribosome translocation arising from experimental facts is that, although the ribosome-mRNA interaction force always has a significant magnitude, the ribosome still moves to the next codon on the mRNA. How does the ribosome move to the next codon in the sequence while holding the mRNA tightly? The hypothesis proposed here is that ribosome subunits alternate the grip of the ribosome on the mRNA, freeing the other subunit of such interaction for a while, thus allowing its motion to the following codon. Based...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Jos é S González-García Source Type: research
Determination of mRNA copy number in degradable lipid nanoparticles via density contrast analytical ultracentrifugation
Eur Biophys J. 2023 Jun 8:1-8. doi: 10.1007/s00249-023-01663-y. Online ahead of print.ABSTRACTLipid nanoparticles as delivery system for mRNA have recently attracted attention to a broader audience as COVID-19 mRNA vaccines. Their low immunogenicity and capability to deliver a variety of nucleic acids renders them an interesting and complementary alternative to gene therapy vectors like AAVs. An important quality attribute of LNPs is the copy number of the encapsulated cargo molecule. This work describes how density and molecular weight distributions obtained by density contrast sedimentation velocity can be used to calcul...
Source: European Biophysics Journal : EBJ - June 8, 2023 Category: Physics Authors: Alexander Bepperling Gesa Richter Source Type: research
