Machine learning based methods to generate conformational ensembles of disordered proteins
Biophys J. 2023 Dec 4:S0006-3495(23)04121-8. doi: 10.1016/j.bpj.2023.12.001. Online ahead of print.ABSTRACTIntrinsically disordered proteins are characterized by a conformational ensemble. While computational approaches such as molecular dynamics simulations have been used to generate such ensembles, their computational costs can be prohibitive. An alternative approach is to learn from data and train machine learning models to generate conformational ensembles of disordered proteins. This has been a relatively unexplored approach, and in this work we demonstrate a proof-of-principle approach to do so. Specifically, we devi...
Source: Biophysical Journal - December 6, 2023 Category: Physics Authors: Ishan Taneja Keren Lasker Source Type: research

Deep learning reduces data requirements and allows real-time measurements in Imaging FCS
Biophys J. 2023 Dec 4:S0006-3495(23)04119-X. doi: 10.1016/j.bpj.2023.11.3403. Online ahead of print.ABSTRACTImaging Fluorescence Correlation Spectroscopy (Imaging FCS) is a powerful tool to extract information on molecular mobilities, actions and interactions in live cells, tissues and organisms. Nevertheless, several limitations restrict its applicability. First, FCS is data hungry, requiring 50,000 frames at 1 ms time resolution to obtain accurate parameter estimates. Second, the data size makes evaluation slow. Thirdly, as FCS evaluation is model-dependent, data evaluation is significantly slowed unless analytic models ...
Source: Biophysical Journal - December 5, 2023 Category: Physics Authors: Wai Hoh Tang Shao Ren Sim Daniel Ying Kia Aik Ashwin Venkata Subba Nelanuthala Thamarailingam Athilingam Adrian R öllin Thorsten Wohland Source Type: research

Deep learning reduces data requirements and allows real-time measurements in Imaging FCS
Biophys J. 2023 Dec 4:S0006-3495(23)04119-X. doi: 10.1016/j.bpj.2023.11.3403. Online ahead of print.ABSTRACTImaging Fluorescence Correlation Spectroscopy (Imaging FCS) is a powerful tool to extract information on molecular mobilities, actions and interactions in live cells, tissues and organisms. Nevertheless, several limitations restrict its applicability. First, FCS is data hungry, requiring 50,000 frames at 1 ms time resolution to obtain accurate parameter estimates. Second, the data size makes evaluation slow. Thirdly, as FCS evaluation is model-dependent, data evaluation is significantly slowed unless analytic models ...
Source: Biophysical Journal - December 5, 2023 Category: Physics Authors: Wai Hoh Tang Shao Ren Sim Daniel Ying Kia Aik Ashwin Venkata Subba Nelanuthala Thamarailingam Athilingam Adrian R öllin Thorsten Wohland Source Type: research

Structural mapping of patient-associated KCNMA1 gene variants
In this study, 82 nonsynonymous patient-associated KCNMA1 variants were mapped within the BK channel protein. Fifty-three variants localized within cryo-EM resolved structures, including 21 classified as either gain-of-function (GOF) or loss-of-function (LOF) in BK channel activity. Clusters of LOF variants were identified in the pore, the AC region (RCK1), and near the Ca2+ bowl (RCK2), overlapping with sites of pharmacological or endogenous modulation. However, no clustering was found for GOF variants. To further understand variants of uncertain significance (VUS), assessments by multiple standard pathogenicity algorithm...
Source: Biophysical Journal - December 3, 2023 Category: Physics Authors: Hans J Moldenhauer Kelly Tammen Andrea L Meredith Source Type: research

Characterization of a novel MgtE homolog and its structural dynamics in membrane-mimetics
Biophys J. 2023 Dec 1:S0006-3495(23)04118-8. doi: 10.1016/j.bpj.2023.11.3402. Online ahead of print.ABSTRACTMagnesium (Mg2+) is the most abundant divalent cation in the cell and is critical for numerous cellular processes. Despite its importance, the mechanisms of intracellular Mg2+ transport and its regulation are poorly understood. MgtE is the main Mg2+ transport system in almost half of bacterial species, and is an ortholog of mammalian SLC41A1 transporters, which are implicated in neurodegenerative diseases and cancer. Till date, only MgtE from Thermus thermophilus (MgtETT) has been extensively characterized mostly in ...
Source: Biophysical Journal - December 3, 2023 Category: Physics Authors: Rupasree Brahma H Raghuraman Source Type: research

Structural mapping of patient-associated KCNMA1 gene variants
In this study, 82 nonsynonymous patient-associated KCNMA1 variants were mapped within the BK channel protein. Fifty-three variants localized within cryo-EM resolved structures, including 21 classified as either gain-of-function (GOF) or loss-of-function (LOF) in BK channel activity. Clusters of LOF variants were identified in the pore, the AC region (RCK1), and near the Ca2+ bowl (RCK2), overlapping with sites of pharmacological or endogenous modulation. However, no clustering was found for GOF variants. To further understand variants of uncertain significance (VUS), assessments by multiple standard pathogenicity algorithm...
Source: Biophysical Journal - December 3, 2023 Category: Physics Authors: Hans J Moldenhauer Kelly Tammen Andrea L Meredith Source Type: research

Characterization of a novel MgtE homolog and its structural dynamics in membrane-mimetics
Biophys J. 2023 Dec 1:S0006-3495(23)04118-8. doi: 10.1016/j.bpj.2023.11.3402. Online ahead of print.ABSTRACTMagnesium (Mg2+) is the most abundant divalent cation in the cell and is critical for numerous cellular processes. Despite its importance, the mechanisms of intracellular Mg2+ transport and its regulation are poorly understood. MgtE is the main Mg2+ transport system in almost half of bacterial species, and is an ortholog of mammalian SLC41A1 transporters, which are implicated in neurodegenerative diseases and cancer. Till date, only MgtE from Thermus thermophilus (MgtETT) has been extensively characterized mostly in ...
Source: Biophysical Journal - December 3, 2023 Category: Physics Authors: Rupasree Brahma H Raghuraman Source Type: research

New and Notable: Revisiting the "Two Cultures" Through Extrinsic Noise
Biophys J. 2023 Nov 30:S0006-3495(23)04116-4. doi: 10.1016/j.bpj.2023.11.3400. Online ahead of print.NO ABSTRACTPMID:38041403 | DOI:10.1016/j.bpj.2023.11.3400 (Source: Biophysical Journal)
Source: Biophysical Journal - December 2, 2023 Category: Physics Authors: Gennady Gorin Lior Pachter Source Type: research

Short disordered N-termini & amp; proline-rich domain are major regulators of UBQLN1/2/4 phase separation
Biophys J. 2023 Nov 30:S0006-3495(23)04117-6. doi: 10.1016/j.bpj.2023.11.3401. Online ahead of print.ABSTRACTHighly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct pha...
Source: Biophysical Journal - December 2, 2023 Category: Physics Authors: Thuy P Dao Anitha Rajendran Sarasi K K Galagedera William Haws Carlos A Casta ñeda Source Type: research

New and Notable: Revisiting the "Two Cultures" Through Extrinsic Noise
Biophys J. 2023 Nov 30:S0006-3495(23)04116-4. doi: 10.1016/j.bpj.2023.11.3400. Online ahead of print.NO ABSTRACTPMID:38041403 | DOI:10.1016/j.bpj.2023.11.3400 (Source: Biophysical Journal)
Source: Biophysical Journal - December 2, 2023 Category: Physics Authors: Gennady Gorin Lior Pachter Source Type: research

Short disordered N-termini & amp; proline-rich domain are major regulators of UBQLN1/2/4 phase separation
Biophys J. 2023 Nov 30:S0006-3495(23)04117-6. doi: 10.1016/j.bpj.2023.11.3401. Online ahead of print.ABSTRACTHighly homologous ubiquitin-binding shuttle proteins UBQLN1, UBQLN2 and UBQLN4 differ in both their specific protein quality control functions and their propensities to localize to stress-induced condensates, cellular aggregates and aggresomes. We previously showed that UBQLN2 phase separates in vitro, and that the phase separation propensities of UBQLN2 deletion constructs correlate with their ability to form condensates in cells. Here, we demonstrated that full-length UBQLN1, UBQLN2 and UBQLN4 exhibit distinct pha...
Source: Biophysical Journal - December 2, 2023 Category: Physics Authors: Thuy P Dao Anitha Rajendran Sarasi K K Galagedera William Haws Carlos A Casta ñeda Source Type: research

N-Glycosylation-dependent regulation of immune-specific tetraspanins CD37 and CD53
In this study we investigated the effects of glycosylation of CD37 and CD53, two tetraspanins important for cellular and humoral immunity. Broad and cell-specific repertoires of N-glycosylated CD37 and CD53 were observed in human B cells. We generated different glycosylation mutants of CD37 and CD53 and analyzed their localization, nanoscale plasma membrane organization and partner protein interaction capacity. Abrogation of glycosylation in CD37 revealed the importance of this modification for CD37 surface expression, whereas surface expression of CD53 was unaffected by its glycosylation. Single-molecule dSTORM microscopy...
Source: Biophysical Journal - November 30, 2023 Category: Physics Authors: Sjoerd van Deventer Ilse A Hoogvliet Merel van de Voort Frank Arnold Martin Ter Beest Annemiek B van Spriel Source Type: research

N-Glycosylation-dependent regulation of immune-specific tetraspanins CD37 and CD53
In this study we investigated the effects of glycosylation of CD37 and CD53, two tetraspanins important for cellular and humoral immunity. Broad and cell-specific repertoires of N-glycosylated CD37 and CD53 were observed in human B cells. We generated different glycosylation mutants of CD37 and CD53 and analyzed their localization, nanoscale plasma membrane organization and partner protein interaction capacity. Abrogation of glycosylation in CD37 revealed the importance of this modification for CD37 surface expression, whereas surface expression of CD53 was unaffected by its glycosylation. Single-molecule dSTORM microscopy...
Source: Biophysical Journal - November 30, 2023 Category: Physics Authors: Sjoerd van Deventer Ilse A Hoogvliet Merel van de Voort Frank Arnold Martin Ter Beest Annemiek B van Spriel Source Type: research

Membrane extraction in native lipid nanodiscs reveals dynamic regulation of Cdc42 complexes during cell polarization
Biophys J. 2023 Nov 23:S0006-3495(23)00721-X. doi: 10.1016/j.bpj.2023.11.021. Online ahead of print.ABSTRACTEmbryonic development requires the establishment of cell polarity to enable cell fate segregation and tissue morphogenesis. This process is regulated by Par complex proteins, which partition into polarized membrane domains and direct downstream polarized cell behaviors. The kinase aPKC (along with its cofactor Par6) is a key member of this network and can be recruited to the plasma membrane by either the small GTPase Cdc42 or the scaffolding protein Par3. Although in vitro interactions among these proteins are well e...
Source: Biophysical Journal - November 25, 2023 Category: Physics Authors: Lars N Deutz Sena Sar ıkaya Daniel J Dickinson Source Type: research

Molecular insight into how the position of an abasic site modifies DNA duplex stability and dynamics
Biophys J. 2023 Nov 23:S0006-3495(23)00722-1. doi: 10.1016/j.bpj.2023.11.022. Online ahead of print.ABSTRACTLocal perturbations to DNA base-pairing stability from lesions and chemical modifications can alter the stability and dynamics of an entire oligonucleotide. End effects may cause the position of a disruption within a short duplex to influence duplex stability and structural dynamics, yet this aspect of nucleic acid modifications is often overlooked. We investigate how the position of an abasic site (AP site) impacts the stability and dynamics of short DNA duplexes. Using a combination of steady-state and time-resolve...
Source: Biophysical Journal - November 25, 2023 Category: Physics Authors: Brennan Ashwood Michael S Jones Yumin Lee Joseph R Sachleben Andrew L Ferguson Andrei Tokmakoff Source Type: research