Energy landscapes for proteins described by the UNRES coarse-grained potential
Biophys Chem. 2023 Sep 12;303:107107. doi: 10.1016/j.bpc.2023.107107. Online ahead of print.ABSTRACTThe self-assembly of proteins is encoded in the underlying potential energy surface (PES), from which we can predict structure, dynamics, and thermodynamic properties. However, the corresponding analysis becomes increasingly challenging with larger protein sizes, due to the computational time required, which grows significantly with the number of atoms. Coarse-grained models offer an attractive approach to reduce the computational cost. In this Feature Article, we describe our implementation of the UNited RESidue (UNRES) coa...
Source: Biophysical Chemistry - October 20, 2023 Category: Chemistry Authors: Patryk A Weso łowski Adam K Sieradzan Micha ł J Winnicki John W R Morgan David J Wales Source Type: research
Energy landscapes for proteins described by the UNRES coarse-grained potential
Biophys Chem. 2023 Sep 12;303:107107. doi: 10.1016/j.bpc.2023.107107. Online ahead of print.ABSTRACTThe self-assembly of proteins is encoded in the underlying potential energy surface (PES), from which we can predict structure, dynamics, and thermodynamic properties. However, the corresponding analysis becomes increasingly challenging with larger protein sizes, due to the computational time required, which grows significantly with the number of atoms. Coarse-grained models offer an attractive approach to reduce the computational cost. In this Feature Article, we describe our implementation of the UNited RESidue (UNRES) coa...
Source: Biophysical Chemistry - October 20, 2023 Category: Chemistry Authors: Patryk A Weso łowski Adam K Sieradzan Micha ł J Winnicki John W R Morgan David J Wales Source Type: research
Charge within Nt17 peptides modulates huntingtin aggregation and initial lipid binding events
Biophys Chem. 2023 Oct 12;303:107123. doi: 10.1016/j.bpc.2023.107123. Online ahead of print.ABSTRACTToxic aggregation of pathogenic huntingtin protein (htt) is implicated in Huntington's disease and influenced by various factors, including the first seventeen amino acids at the N-terminus (Nt17) and the presence of lipid membranes. Nt17 has a propensity to form an amphipathic α-helix in the presence of binding partners, which promotes α-helix rich oligomer formation and facilitates htt/lipid interactions. Within Nt17 are multiple sites that are subject to post-translational modification, including acetylation and phospho...
Source: Biophysical Chemistry - October 18, 2023 Category: Chemistry Authors: Alyssa R Stonebraker Rachel Hankin Kathryn L Kapp Peng Li Stephen J Valentine Justin Legleiter Source Type: research
Charge within Nt17 peptides modulates huntingtin aggregation and initial lipid binding events
Biophys Chem. 2023 Oct 12;303:107123. doi: 10.1016/j.bpc.2023.107123. Online ahead of print.ABSTRACTToxic aggregation of pathogenic huntingtin protein (htt) is implicated in Huntington's disease and influenced by various factors, including the first seventeen amino acids at the N-terminus (Nt17) and the presence of lipid membranes. Nt17 has a propensity to form an amphipathic α-helix in the presence of binding partners, which promotes α-helix rich oligomer formation and facilitates htt/lipid interactions. Within Nt17 are multiple sites that are subject to post-translational modification, including acetylation and phospho...
Source: Biophysical Chemistry - October 18, 2023 Category: Chemistry Authors: Alyssa R Stonebraker Rachel Hankin Kathryn L Kapp Peng Li Stephen J Valentine Justin Legleiter Source Type: research
The interaction between alpha-synuclein and mitochondrial dysfunction in Parkinson's disease
Biophys Chem. 2023 Oct 10;303:107122. doi: 10.1016/j.bpc.2023.107122. Online ahead of print.ABSTRACTParkinson's disease (PD) is an aging-associated neurodegenerative disorder with the hallmark of abnormal aggregates of alpha-synuclein (α-syn) in Lewy bodies (LBs) and Lewy neurites (LNs). Currently, pathogenic α-syn and mitochondrial dysfunction have been considered as prominent roles that give impetus to the PD onset. This review describes the α-syn pathology and mitochondrial alterations in PD, and focuses on how α-syn interacts with multiple aspects of mitochondrial homeostasis in the pathogenesis of PD.PMID:37839353...
Source: Biophysical Chemistry - October 15, 2023 Category: Chemistry Authors: Hong-Yan Li De-Shui Liu Ying-Bo Zhang Hua Rong Xiao-Jie Zhang Source Type: research
The interaction between alpha-synuclein and mitochondrial dysfunction in Parkinson's disease
Biophys Chem. 2023 Oct 10;303:107122. doi: 10.1016/j.bpc.2023.107122. Online ahead of print.ABSTRACTParkinson's disease (PD) is an aging-associated neurodegenerative disorder with the hallmark of abnormal aggregates of alpha-synuclein (α-syn) in Lewy bodies (LBs) and Lewy neurites (LNs). Currently, pathogenic α-syn and mitochondrial dysfunction have been considered as prominent roles that give impetus to the PD onset. This review describes the α-syn pathology and mitochondrial alterations in PD, and focuses on how α-syn interacts with multiple aspects of mitochondrial homeostasis in the pathogenesis of PD.PMID:37839353...
Source: Biophysical Chemistry - October 15, 2023 Category: Chemistry Authors: Hong-Yan Li De-Shui Liu Ying-Bo Zhang Hua Rong Xiao-Jie Zhang Source Type: research
The interaction between alpha-synuclein and mitochondrial dysfunction in Parkinson's disease
Biophys Chem. 2023 Oct 10;303:107122. doi: 10.1016/j.bpc.2023.107122. Online ahead of print.ABSTRACTParkinson's disease (PD) is an aging-associated neurodegenerative disorder with the hallmark of abnormal aggregates of alpha-synuclein (α-syn) in Lewy bodies (LBs) and Lewy neurites (LNs). Currently, pathogenic α-syn and mitochondrial dysfunction have been considered as prominent roles that give impetus to the PD onset. This review describes the α-syn pathology and mitochondrial alterations in PD, and focuses on how α-syn interacts with multiple aspects of mitochondrial homeostasis in the pathogenesis of PD.PMID:37839353...
Source: Biophysical Chemistry - October 15, 2023 Category: Chemistry Authors: Hong-Yan Li De-Shui Liu Ying-Bo Zhang Hua Rong Xiao-Jie Zhang Source Type: research
In-silicon studies on hydration in EcoRI-cognate DNA complex
Biophys Chem. 2023 Oct 6;303:107121. doi: 10.1016/j.bpc.2023.107121. Online ahead of print.ABSTRACTRestriction endonucleases (REs) cleave DNA at specific site in presence of Mg2+ ion. Experiments further emphasize the role of hydration in metal ion specificity and sequence specificity of DNA cleavage. However, the relation between hydration and specificity has not been understood till date. This leads us to study via all-atom molecular dynamics (MD) simulations how the hydration around the scissile phosphate group changes in presence of Mg2+ and Ca2+ and depend on the DNA sequence. We observe the least number of hydrogen b...
Source: Biophysical Chemistry - October 14, 2023 Category: Chemistry Authors: Sasthi Charan Mandal Jaydeb Chakrabarti Source Type: research
Nitric oxide modulates NMDA receptor through a negative feedback mechanism and regulates the dynamical behavior of neuronal postsynaptic components
Biophys Chem. 2023 Sep 27;303:107114. doi: 10.1016/j.bpc.2023.107114. Online ahead of print.ABSTRACTNitric oxide (NO) is known to be an important regulator of neurological processes in the central nervous system which acts directly on the presynaptic neuron and enhances the release of neurotransmitters like glutamate into the synaptic cleft. Calcium influx activates a cascade of biochemical reactions to influence the production of nitric oxide in the postsynaptic neuron. This has been modeled in the present work as a system of ordinary differential equations, to explore the dynamics of the interacting components and predic...
Source: Biophysical Chemistry - October 13, 2023 Category: Chemistry Authors: Bhanu Sharma Daniel Tuikhang Koren Subhendu Ghosh Source Type: research
Nitric oxide modulates NMDA receptor through a negative feedback mechanism and regulates the dynamical behavior of neuronal postsynaptic components
Biophys Chem. 2023 Sep 27;303:107114. doi: 10.1016/j.bpc.2023.107114. Online ahead of print.ABSTRACTNitric oxide (NO) is known to be an important regulator of neurological processes in the central nervous system which acts directly on the presynaptic neuron and enhances the release of neurotransmitters like glutamate into the synaptic cleft. Calcium influx activates a cascade of biochemical reactions to influence the production of nitric oxide in the postsynaptic neuron. This has been modeled in the present work as a system of ordinary differential equations, to explore the dynamics of the interacting components and predic...
Source: Biophysical Chemistry - October 13, 2023 Category: Chemistry Authors: Bhanu Sharma Daniel Tuikhang Koren Subhendu Ghosh Source Type: research
Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane
Biophys Chem. 2023 Sep 25;303:107113. doi: 10.1016/j.bpc.2023.107113. Online ahead of print.ABSTRACTThe mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-...
Source: Biophysical Chemistry - October 1, 2023 Category: Chemistry Authors: Aleksi Sutinen Nykola C Jones S øren Vrønning Hoffmann Salla Ruskamo Petri Kursula Source Type: research
Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane
Biophys Chem. 2023 Sep 25;303:107113. doi: 10.1016/j.bpc.2023.107113. Online ahead of print.ABSTRACTThe mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-...
Source: Biophysical Chemistry - October 1, 2023 Category: Chemistry Authors: Aleksi Sutinen Nykola C Jones S øren Vrønning Hoffmann Salla Ruskamo Petri Kursula Source Type: research
Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane
Biophys Chem. 2023 Sep 25;303:107113. doi: 10.1016/j.bpc.2023.107113. Online ahead of print.ABSTRACTThe mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-...
Source: Biophysical Chemistry - October 1, 2023 Category: Chemistry Authors: Aleksi Sutinen Nykola C Jones S øren Vrønning Hoffmann Salla Ruskamo Petri Kursula Source Type: research
Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane
Biophys Chem. 2023 Sep 25;303:107113. doi: 10.1016/j.bpc.2023.107113. Online ahead of print.ABSTRACTThe mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-...
Source: Biophysical Chemistry - October 1, 2023 Category: Chemistry Authors: Aleksi Sutinen Nykola C Jones S øren Vrønning Hoffmann Salla Ruskamo Petri Kursula Source Type: research
Conformational analysis of membrane-proximal segments of GDAP1 in a lipidic environment using synchrotron radiation suggests a mode of assembly at the mitochondrial outer membrane
Biophys Chem. 2023 Sep 25;303:107113. doi: 10.1016/j.bpc.2023.107113. Online ahead of print.ABSTRACTThe mitochondrial outer membrane creates a diffusion barrier between the cytosol and the mitochondrial intermembrane space, allowing the exchange of metabolic products, important for efficient mitochondrial function in neurons. The ganglioside-induced differentiation-associated protein 1 (GDAP1) is a mitochondrial outer membrane protein with a critical role in mitochondrial dynamics and metabolic balance in neurons. Missense mutations in the GDAP1 gene are linked to the most common human peripheral neuropathy, Charcot-Marie-...
Source: Biophysical Chemistry - October 1, 2023 Category: Chemistry Authors: Aleksi Sutinen Nykola C Jones S øren Vrønning Hoffmann Salla Ruskamo Petri Kursula Source Type: research
