GABA < sub > A < /sub > receptor subunit M2-M3 linkers have asymmetric roles in pore gating and diazepam modulation
Biophys J. 2024 Feb 22:S0006-3495(24)00136-X. doi: 10.1016/j.bpj.2024.02.016. Online ahead of print.ABSTRACTGABAA receptors (GABAARs) are neurotransmitter-gated ion channels critical for inhibitory synaptic transmission as well as the molecular target for benzodiazepines (BZDs), one of the most widely prescribed class of psychotropic drugs today. Despite structural insight into the conformations underlying functional channel states, the detailed molecular interactions involved in conformational transitions and the physical basis for their modulation by BZDs are not fully understood. We previously identified that alanine su...
Source: Biophysical Journal - February 24, 2024 Category: Physics Authors: Joseph W Nors Zachary Endres Marcel P Goldschen-Ohm Source Type: research
Redox dependent Cd < sup > 2+ < /sup > inhibition of BK type Ca < sup > 2+ < /sup > activated K < sup > + < /sup > channels
Biophys J. 2024 Feb 22:S0006-3495(24)00135-8. doi: 10.1016/j.bpj.2024.02.015. Online ahead of print.ABSTRACTLarge conductance Ca2+-activated K+ channels (BK channels) are formed by Slo1 subunits as a homotetramer. Besides Ca2+, other divalent cations, such as Cd2+, also activate BK channels when applied intracellularly by shifting the conductance-voltage (GV) relation to more negative voltages. However, we found that if the inside-out patch containing BK channels was treated with solution containing reducing agents such as DTT subsequent Cd2+ application completely inhibited BK currents. The DTT dependent Cd2+ inhibition c...
Source: Biophysical Journal - February 24, 2024 Category: Physics Authors: Guohui Zhang Huanghe Yang Yuyin Wang Hongwu Liang Jingyi Shi Jianmin Cui Source Type: research
GABA < sub > A < /sub > receptor subunit M2-M3 linkers have asymmetric roles in pore gating and diazepam modulation
Biophys J. 2024 Feb 22:S0006-3495(24)00136-X. doi: 10.1016/j.bpj.2024.02.016. Online ahead of print.ABSTRACTGABAA receptors (GABAARs) are neurotransmitter-gated ion channels critical for inhibitory synaptic transmission as well as the molecular target for benzodiazepines (BZDs), one of the most widely prescribed class of psychotropic drugs today. Despite structural insight into the conformations underlying functional channel states, the detailed molecular interactions involved in conformational transitions and the physical basis for their modulation by BZDs are not fully understood. We previously identified that alanine su...
Source: Biophysical Journal - February 24, 2024 Category: Physics Authors: Joseph W Nors Zachary Endres Marcel P Goldschen-Ohm Source Type: research
Redox dependent Cd < sup > 2+ < /sup > inhibition of BK type Ca < sup > 2+ < /sup > activated K < sup > + < /sup > channels
Biophys J. 2024 Feb 22:S0006-3495(24)00135-8. doi: 10.1016/j.bpj.2024.02.015. Online ahead of print.ABSTRACTLarge conductance Ca2+-activated K+ channels (BK channels) are formed by Slo1 subunits as a homotetramer. Besides Ca2+, other divalent cations, such as Cd2+, also activate BK channels when applied intracellularly by shifting the conductance-voltage (GV) relation to more negative voltages. However, we found that if the inside-out patch containing BK channels was treated with solution containing reducing agents such as DTT subsequent Cd2+ application completely inhibited BK currents. The DTT dependent Cd2+ inhibition c...
Source: Biophysical Journal - February 24, 2024 Category: Physics Authors: Guohui Zhang Huanghe Yang Yuyin Wang Hongwu Liang Jingyi Shi Jianmin Cui Source Type: research
Machine learning and advanced statistical analysis for Fluorescence Correlation Spectroscopy
Biophys J. 2024 Feb 21:S0006-3495(24)00131-0. doi: 10.1016/j.bpj.2024.02.011. Online ahead of print.NO ABSTRACTPMID:38389302 | DOI:10.1016/j.bpj.2024.02.011 (Source: Biophysical Journal)
Source: Biophysical Journal - February 23, 2024 Category: Physics Authors: J örg Enderlein Source Type: research
Machine learning and advanced statistical analysis for Fluorescence Correlation Spectroscopy
Biophys J. 2024 Feb 21:S0006-3495(24)00131-0. doi: 10.1016/j.bpj.2024.02.011. Online ahead of print.NO ABSTRACTPMID:38389302 | DOI:10.1016/j.bpj.2024.02.011 (Source: Biophysical Journal)
Source: Biophysical Journal - February 23, 2024 Category: Physics Authors: J örg Enderlein Source Type: research
Neural network informed photon filtering reduces fluorescence correlation spectroscopy artifacts
In conclusion, this simulation-based, automated, open-source pipeline makes measurements analyzable which previously had to be discarded and extends every FCS user's experimental toolbox.PMID:38384131 | DOI:10.1016/j.bpj.2024.02.012 (Source: Biophysical Journal)
Source: Biophysical Journal - February 22, 2024 Category: Physics Authors: Alexander Seltmann Pablo Carravilla Katharina Reglinski Christian Eggeling Dominic Waithe Source Type: research
Deep-LASI, Single Molecule Data Analysis Software
Biophys J. 2024 Feb 20:S0006-3495(24)00133-4. doi: 10.1016/j.bpj.2024.02.013. Online ahead of print.ABSTRACTBy avoiding ensemble averaging, single molecule methods provide novel means of extracting mechanistic insights in to function of material and molecules at the nanoscale. However, one of the big limitations is the vast amount of data required for analyzing and extracting the desired information, which is time consuming and user dependent. Here, we introduce Deep-LASI, a software package for the manual and automatic analysis of single molecule traces, interactions and the underlying kinetics. The software can handle da...
Source: Biophysical Journal - February 22, 2024 Category: Physics Authors: Pooyeh Asadiatouei Clemens-B ässem Salem Simon Wanninger Evelyn Ploetz Don C Lamb Source Type: research
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies: You can teach old dogs new tricks
Biophys J. 2024 Feb 20:S0006-3495(24)00134-6. doi: 10.1016/j.bpj.2024.02.014. Online ahead of print.ABSTRACTThe timeless question of whether old dogs can learn new tricks can also be asked for scientific methods. One such example can be found in the article "Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies" by Mayu Shibata and coworkers. In their study the authors show some new tricks using an established method, Direct Coupling Analysis (DCA). So let us dive first into its history.PMID:38379283 | DOI:10.1016/j.bpj.2024.02.014 (Source: Biophysical Journal)
Source: Biophysical Journal - February 21, 2024 Category: Physics Authors: Alexander Schug Source Type: research
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies: You can teach old dogs new tricks
Biophys J. 2024 Feb 20:S0006-3495(24)00134-6. doi: 10.1016/j.bpj.2024.02.014. Online ahead of print.ABSTRACTThe timeless question of whether old dogs can learn new tricks can also be asked for scientific methods. One such example can be found in the article "Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies" by Mayu Shibata and coworkers. In their study the authors show some new tricks using an established method, Direct Coupling Analysis (DCA). So let us dive first into its history.PMID:38379283 | DOI:10.1016/j.bpj.2024.02.014 (Source: Biophysical Journal)
Source: Biophysical Journal - February 21, 2024 Category: Physics Authors: Alexander Schug Source Type: research
Improving cryo-EM grids for amyloid fibrils using interface-active solutions and spectator proteins
Biophys J. 2024 Feb 16:S0006-3495(24)00129-2. doi: 10.1016/j.bpj.2024.02.009. Online ahead of print.ABSTRACTPreparation of cryo-EM grids for imaging of amyloid fibrils is notoriously challenging. The human Islet Amyloid Polypeptide (hIAPP) serves as a notable example, as the majority of reported structures have relied on the use of non-physiological pH buffers, N-terminal tags, and seeding. This highlights the need for more efficient, reproducible methodologies that can elucidate amyloid fibril structures formed under diverse conditions. In this work, we demonstrate that the distribution of fibrils on cryo-EM grids is pred...
Source: Biophysical Journal - February 18, 2024 Category: Physics Authors: Dylan Valli Saik Ann Ooi Giorgio Scattolini Himanshu Chaudhary Alesia A Tietze Micha ł Maj Source Type: research
Improving cryo-EM grids for amyloid fibrils using interface-active solutions and spectator proteins
Biophys J. 2024 Feb 16:S0006-3495(24)00129-2. doi: 10.1016/j.bpj.2024.02.009. Online ahead of print.ABSTRACTPreparation of cryo-EM grids for imaging of amyloid fibrils is notoriously challenging. The human Islet Amyloid Polypeptide (hIAPP) serves as a notable example, as the majority of reported structures have relied on the use of non-physiological pH buffers, N-terminal tags, and seeding. This highlights the need for more efficient, reproducible methodologies that can elucidate amyloid fibril structures formed under diverse conditions. In this work, we demonstrate that the distribution of fibrils on cryo-EM grids is pred...
Source: Biophysical Journal - February 18, 2024 Category: Physics Authors: Dylan Valli Saik Ann Ooi Giorgio Scattolini Himanshu Chaudhary Alesia A Tietze Micha ł Maj Source Type: research
Improving cryo-EM grids for amyloid fibrils using interface-active solutions and spectator proteins
Biophys J. 2024 Feb 16:S0006-3495(24)00129-2. doi: 10.1016/j.bpj.2024.02.009. Online ahead of print.ABSTRACTPreparation of cryo-EM grids for imaging of amyloid fibrils is notoriously challenging. The human Islet Amyloid Polypeptide (hIAPP) serves as a notable example, as the majority of reported structures have relied on the use of non-physiological pH buffers, N-terminal tags, and seeding. This highlights the need for more efficient, reproducible methodologies that can elucidate amyloid fibril structures formed under diverse conditions. In this work, we demonstrate that the distribution of fibrils on cryo-EM grids is pred...
Source: Biophysical Journal - February 18, 2024 Category: Physics Authors: Dylan Valli Saik Ann Ooi Giorgio Scattolini Himanshu Chaudhary Alesia A Tietze Micha ł Maj Source Type: research
An Entropy-Based Approach for Assessing the Directional Persistence of Cell Migration
Biophys J. 2024 Feb 16:S0006-3495(24)00130-9. doi: 10.1016/j.bpj.2024.02.010. Online ahead of print.ABSTRACTCell migration, which is primarily characterized by directional persistence, is essential for the development of normal tissues and organs, as well as for numerous pathological processes. However, there is a lack of simple and efficient tools to analyze the systematic properties of persistence based on cellular trajectory data. Here, we present a novel approach, the Entropy of Angular Distribution (EAD), which combines cellular turning dynamics and Shannon entropy to explore the statistical and time-varying propertie...
Source: Biophysical Journal - February 17, 2024 Category: Physics Authors: Yanping Liu Yang Jiao Xinwei Li Guoqiang Li Wei Wang Zhichao Liu Dui Qin Lisha Zhong Liyu Liu Jianwei Shuai Zhangyong Li Source Type: research
An Entropy-Based Approach for Assessing the Directional Persistence of Cell Migration
Biophys J. 2024 Feb 16:S0006-3495(24)00130-9. doi: 10.1016/j.bpj.2024.02.010. Online ahead of print.ABSTRACTCell migration, which is primarily characterized by directional persistence, is essential for the development of normal tissues and organs, as well as for numerous pathological processes. However, there is a lack of simple and efficient tools to analyze the systematic properties of persistence based on cellular trajectory data. Here, we present a novel approach, the Entropy of Angular Distribution (EAD), which combines cellular turning dynamics and Shannon entropy to explore the statistical and time-varying propertie...
Source: Biophysical Journal - February 17, 2024 Category: Physics Authors: Yanping Liu Yang Jiao Xinwei Li Guoqiang Li Wei Wang Zhichao Liu Dui Qin Lisha Zhong Liyu Liu Jianwei Shuai Zhangyong Li Source Type: research
