Top 6 Biorxiv Papers Today in Biophysics


2.023 Mikeys
#1. An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics
Aoife Martha Harbison, Elisa Fadda
The immunoglobulin type G (IgG) Fc N-glycans are known to modulate the interaction with membrane-bound Fc γ receptors (FcγRs), fine-tuning the antibody effector function in a sequence-dependent manner. Particularly interesting in this respect are the roles of galactosylation, which levels are linked to autoimmune conditions and aging, of core fucosylation, which is known to reduce significantly the antibody-dependent cellular cytotoxicity (ADCC), and of sialylation, which also reduces ADCC but only in the context of core-fucosylation. In this work we provide an atomistic level perspective through enhanced sampling computer simulations, based on replica exchange molecular dynamics (REMD), to understand the molecular determinants linking the Fc N-glycans sequence to the observed IgG1 function. Our results indicate that the two symmetrically opposed N-glycans interact extensively through their core trimannose residues. At room temperature the terminal galactose on the α(1-6) arm is restrained to the protein through a network of...
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biorxivpreprint: An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics https://t.co/OW3A0SO4qA #bioRxiv
biorxiv_biophys: An atomistic perspective on ADCC quenching by core-fucosylation of IgG1 Fc N-glycans from enhanced sampling molecular dynamics https://t.co/cyep46SpQP #biorxiv_biophys
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Sample Sizes : None.
Authors: 2
Total Words: 6345
Unqiue Words: 1871

2.016 Mikeys
#2. RNAPosers: Machine Learning Classifiers For RNA-Ligand Poses
Sahil Chhabra, Jingru Xie, Aaron Terrence Frank
Determining the 3-dimensional (3D) structures of ribonucleic acid (RNA)-small molecule complexes is critical to understanding molecular recognition in RNA. Computer docking can, in principle, be used to predict the 3D structure of RNA-small molecule complexes. Unfortunately, retrospective analysis has shown that the scoring functions that are typically used to rank poses tend to misclassify non-native poses as native, and vice versa . This misclassification of non-native poses severely limits the utility of computer docking in the context pose prediction, as well as in virtual screening. Here, we use machine learning to train a set of pose classifiers that estimate the relative "nativeness" of a set of RNA-ligand poses. At the heart of our approach is the use of a pose "fingerprint" that is a composite of a set of atomic fingerprints, which individually encode the local "RNA environment" around ligand atoms. We found that by ranking poses based on the classification scores from our machine learning classifiers, we were able to...
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biorxivpreprint: RNAPosers: Machine Learning Classifiers For RNA-Ligand Poses https://t.co/totMWCTR0X #bioRxiv
biorxiv_biophys: RNAPosers: Machine Learning Classifiers For RNA-Ligand Poses https://t.co/Nl9GhxJOdf #biorxiv_biophys
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A Set of Machine Learning Classifiers For RNA Containing Complexes

Repository: RNAPosers
User: atfrank
Language: HTML
Stargazers: 0
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Sample Sizes : None.
Authors: 3
Total Words: 7042
Unqiue Words: 1890

2.007 Mikeys
#3. An implicit lipid model for efficient reaction-diffusion simulations of protein binding to surfaces of arbitrary topology
Yiben Fu, Osman N Yogurtcu, Ruchita Kothari, Gudrud Thorkelsdottir, Alexander J Sodt, Margaret E Johnson
Localization of proteins to a membrane is an essential step in a broad range of biological processes such as signaling, virion formation, and clathrin-mediated endocytosis. The strength and specificity of proteins binding to a membrane depend on the lipid composition. Single-particle reaction-diffusion methods offer a powerful tool for capturing lipid-specific binding to membrane surfaces by treating lipids explicitly as individual diffusible binding sites. However, modeling lipid particle populations is expensive. Here we present an algorithm for reversible binding of proteins to continuum surfaces with implicit lipids, providing dramatic speed-ups to many body simulations. Our algorithm can be readily integrated into most reaction-diffusion software packages. We characterize changes to kinetics that emerge from explicit versus implicit lipids as well as surface adsorption models, showing excellent agreement between our method and the full explicit lipid model. Compared to models of surface adsorption, which couple together...
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RD code using the FPR algorithm, with an implicit lipid model for membrane binding

Repository: fpr_implicit
User: mjohn218
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Authors: 6
Total Words: 16740
Unqiue Words: 3483

1.998 Mikeys
#4. Liquid-liquid phase separation and fibrillization of tau are independent processes with overlapping conditions
Yanxian Lin, Yann Fichou, Zhikai Zeng, Nicole Y. Hu, Songi Han
Amyloid aggregation of the microtubule binding protein tau is a hallmark of Alzheimer's disease and many other neurodegenerative diseases. Recently, tau has been found to undergo liquid-liquid phase separation (LLPS) near physiological conditions. Although LLPS and aggregation have been shown to simultaneously occur under certain common conditions, it remains to be seen whether tau LLPS promotes aggregation, or if they are two independent processes. In this study, we address this question by combining multiple biochemical and biophysical assays in vitro. We investigated the impacts of LLPS on tau aggregation at three stages: conformation of tau, kinetics of aggregation and fibril quantity. We showed that none of these properties are influenced directly by LLPS, while amyloid aggregation propensity of tau can be altered without affecting its LLPS behavior. LLPS and amyloid aggregation of tau occur under overlapping conditions of enhanced intermolecular interactions and localization, but are two independent processes.
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biorxivpreprint: Liquid-liquid phase separation and fibrillization of tau are independent processes with overlapping conditions https://t.co/fdyIEdf3AU #bioRxiv
biorxiv_biophys: Liquid-liquid phase separation and fibrillization of tau are independent processes with overlapping conditions https://t.co/rhalbEyien #biorxiv_biophys
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Sample Sizes : [485, 485, 485]
Authors: 5
Total Words: 10865
Unqiue Words: 2952

1.998 Mikeys
#5. Phospholamban and sarcolipin share similar transmembrane zipper motifs that control self-association affinity and oligomer stoichiometry
Nicholas R. DesLauriers, Bengt Svensson, David D. Thomas, Joseph M. Autry
We have characterized the structural determinants of phospholamban (PLB) and sarcolipin (SLN) self-association using site-directed mutagenesis, SDS-PAGE, and fluorescence resonance energy transfer (FRET) microscopy. PLB and SLN are single-pass transmembrane (TM) peptides that are critically involved in regulation of contractility in cardiac and skeletal muscle via reversible inhibition of calcium (Ca) transport by SERCA. PLB and SLN also exhibit ion channel activity in vitro, yet the physiological significance of these functions is unknown. Here we have determined that structural insights offered by the tetrameric PLB Cys41 to Leu (C41L) mutation, a mutant with four possible leucine/isoleucine zipper interactions for stabilizing PLB tetramers. Using scanning alanine mutagenesis and SDS-PAGE, we have determined the C41L-PLB tetramer is destabilized by mutation of Leu37 to Ala (L37A) or Ile40 to Ala (I40A), which are the same a- and d-arm residues stabilizing the PLB pentamer via leucine/isoleucine zippers, highlighting the...
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biorxivpreprint: Phospholamban and sarcolipin share similar transmembrane zipper motifs that control self-association affinity and oligomer stoichiometry https://t.co/kLKYfokUVr #bioRxiv
biorxiv_biophys: Phospholamban and sarcolipin share similar transmembrane zipper motifs that control self-association affinity and oligomer stoichiometry https://t.co/E9mCNiksv5 #biorxiv_biophys
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Authors: 4
Total Words: 8327
Unqiue Words: 2472

1.998 Mikeys
#6. High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities
Alexander J Bryer, Jodi A. Hadden, John E. Stone, Juan R Perilla
Compartmentalization is a central theme in biology. Cells are composed of numerous membrane-enclosed structures, evolved to facilitate specific biochemical processes; viruses act as containers of genetic material, optimized to drive infection. Molecular dynamics simulations provide a mechanism to study biomolecular containers and the influence they exert on their environments; however, trajectory analysis software generally lacks knowledge of container interior versus exterior. Further, many relevant container analyses involve large-scale particle tracking endeavors, which may become computationally prohibitive with increasing system size. Here, a novel method based on 3-D ray casting is presented, which rapidly classifies the space surrounding biomolecular containers of arbitrary shape, enabling fast determination of the identities and counts of particles (e.g., solvent molecules) found inside and outside. The method is broadly applicable to the study of containers and enables high-performance characterization of properties such...
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biorxivpreprint: High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein cavities https://t.co/1sPaTICvBT #bioRxiv
biorxiv_biophys: High-performance analysis of biomolecular containers to measure small-molecule transport, transbilayer lipid diffusion, and protein ... https://t.co/sDcnCzVUUW #biorxiv_biophys
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Sample Sizes : [2, 64, 32, 12]
Authors: 4
Total Words: 12285
Unqiue Words: 3512

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