scholarly journals Recovery of conformational continuum from single-particle cryo-EM data: Optimization of ManifoldEM informed by ground-truth studies

2021 ◽  
Author(s):  
Evan Seitz ◽  
Peter Schwander ◽  
Francisco J. Acosta-Reyes ◽  
Suvrajit Maji ◽  
Joachim Frank
Keyword(s):  
Conformational Changes ◽  
Degrees Of Freedom ◽  
Ground Truth ◽  
Biological Molecules ◽  
Geometric Information ◽  
New Approach ◽  
Manifold Embedding ◽  
Latent Space ◽  
Wide Range ◽  
Heuristic Analysis

This work is based on the manifold-embedding approach to the study of biological molecules exhibiting conformational changes in a continuum. Previous studies established a workflow capable of reconstructing atomic-level structures in the conformational continuum from cryo-EM images so as to reveal the latent space of macromolecules undergoing multiple degrees of freedom. Here, we introduce a new approach that is informed by detailed heuristic analysis of manifolds formed by simulated heterogeneous cryo-EM datasets. These simulated models were generated with increasing complexity to account for multiple motions, state occupancies and CTF in a wide range of signal-to-noise ratios. Using these datasets as ground-truth, we provide detailed exposition of our findings using several conformational motions while exploring the available parameter space. Guided by these insights, we build a framework to leverage the high-dimensional geometric information obtained towards reconstituting the quasi-continuum of conformational states in the form of an energy landscape and respective 3D maps for all states therein. This framework offers substantial enhancements relative to previous work, for which a direct comparison of outputs has been provided.

scholarly journals Functional Pathways of Biomolecules Retrieved from Single-particle Snapshots

2018 ◽  
Author(s):  
A. Dashti ◽  
M.S. Shekhar ◽  
D. Ben Hail ◽  
G. Mashayekhi ◽  
P. Schwander ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Single Particle ◽  
Biological Function ◽  
Energy Landscapes ◽  
Structural Domains ◽  
New Approach ◽  
Contraction Coupling ◽  
Gating Mechanism ◽  
Wide Range ◽  
Discrete Structures

AbstractWe present a new approach to determining the conformational changes associated with biological function, and demonstrate its capabilities in the context of experimental single-particle cryo-EM snapshots of ryanodine receptor (RyR1), a Ca2+-channel involved in skeletal muscle excitation/contraction coupling. These results include the detailed conformational motions associated with functional paths including transitions between energy landscapes. The functional motions differ substantially from those inferred from discrete structures, shedding new light on the gating mechanism in RyR1. The differences include the conformationally active structural domains, the nature, sequence, and extent of conformational motions involved in function, and the way allosteric signals are transduced within and between domains. The approach is general, and applicable to a wide range of systems and processes.

High Reconfigurable Robotic Gripper for Flexible Assembly

2014 ◽  
Author(s):  
C. Canali ◽  
F. Cannella ◽  
F. Chen ◽  
T. Hauptman ◽  
G. Sofia ◽  
...  
Keyword(s):  
Degrees Of Freedom ◽  
General Purpose ◽  
Test Rig ◽  
New Approach ◽  
Factory Automation ◽  
Flexible Assembly ◽  
Industrial Manufacturing ◽  
Adaptive Capabilities ◽  
Wide Range ◽  
Complicated Geometry

This paper describes a general purpose gripper to be used into industrial manufacturing application. The gripper has been developed in the context of the AUTORECON project. It is based on a 2 degrees of freedom finger that is able to adapt itself to objects of various shape, size, material and weight. Thanks to its highly reconfigurable and adaptive capabilities, the gripper described here is an attempt to create a gripper suitable in industrial application to assemble compounds of several different workpieces using only one robot. The high dexterity and the wide range of possible uses of the gripper described here intends to explore a new approach to the design of industrial grippers to be used in factory automation. Moreover, the adaptive capabilities of this gripper make it suitable to grasp workpieces with complicated geometry or highly irregular shape, as it has been proved in performed automotive test rig described here.

scholarly journals Simulation of cryo-EM ensembles from atomic models of molecules exhibiting continuous conformations

2019 ◽  
Author(s):  
Evan Seitz ◽  
Francisco Acosta-Reyes ◽  
Peter Schwander ◽  
Joachim Frank
Keyword(s):  
Single Molecule ◽  
Conformational Changes ◽  
Degrees Of Freedom ◽  
Ground Truth ◽  
Free Energies ◽  
Ground Truth Data ◽  
Metabolic Functions ◽  
In Vitro Systems ◽  
Low Dimensional

AbstractMolecular machines visit a continuum of conformational states as they go through work cycles required for their metabolic functions. Single-molecule cryo-EM of suitable in vitro systems affords the ability to collect a large ensemble of projections depicting the continuum of structures and assign occupancies, or free energies, to the observed states. Through the use of machine learning and dimension reduction algorithms it is possible to determine a low-dimensional free energy landscape from such data, allowing the basis for molecular function to be elucidated. In the absence of ground truth data, testing and validation of such methods is quite difficult, however. In this work, we propose a workflow for generating simulated cryo-EM data from an atomic model subjected to conformational changes. As an example, an ensemble of structures and their multiple projections was created from heat shock protein Hsp90 with two defined conformational degrees of freedom. All scripts for reproducing this workflow are available online. 1

scholarly journals CFNet: LiDAR-Camera Registration Using Calibration Flow Network

Sensors ◽  
2021 ◽  
Vol 21 (23) ◽  
pp. 8112
Author(s):  
Xudong Lv ◽  
Shuo Wang ◽  
Dong Ye
Keyword(s):  
Autonomous Vehicles ◽  
Degrees Of Freedom ◽  
Image Data ◽  
Ground Truth ◽  
Geometric Information ◽  
Six Degrees Of Freedom ◽  
Calibration Methods ◽  
Extrinsic Parameters ◽  
Calibration Algorithm ◽  
Complex Optimization

As an essential procedure of data fusion, LiDAR-camera calibration is critical for autonomous vehicles and robot navigation. Most calibration methods require laborious manual work, complicated environmental settings, and specific calibration targets. The targetless methods are based on some complex optimization workflow, which is time-consuming and requires prior information. Convolutional neural networks (CNNs) can regress the six degrees of freedom (6-DOF) extrinsic parameters from raw LiDAR and image data. However, these CNN-based methods just learn the representations of the projected LiDAR and image and ignore the correspondences at different locations. The performances of these CNN-based methods are unsatisfactory and worse than those of non-CNN methods. In this paper, we propose a novel CNN-based LiDAR-camera extrinsic calibration algorithm named CFNet. We first decided that a correlation layer should be used to provide matching capabilities explicitly. Then, we innovatively defined calibration flow to illustrate the deviation of the initial projection from the ground truth. Instead of directly predicting the extrinsic parameters, we utilize CFNet to predict the calibration flow. The efficient Perspective-n-Point (EPnP) algorithm within the RANdom SAmple Consensus (RANSAC) scheme is applied to estimate the extrinsic parameters with 2D–3D correspondences constructed by the calibration flow. Due to its consideration of the geometric information, our proposed method performed better than the state-of-the-art CNN-based methods on the KITTI datasets. Furthermore, we also tested the flexibility of our approach on the KITTI360 datasets.

scholarly journals GUV-Net for high fidelity shoeprint generation

2021 ◽  
Author(s):  
Muhammad Hassan ◽  
Yan Wang ◽  
Wei Pang ◽  
Di Wang ◽  
Daixi Li ◽  
...  
Keyword(s):  
Deep Learning ◽  
Dimensional Space ◽  
Super Resolution ◽  
Network Models ◽  
Ground Truth ◽  
Special Treatment ◽  
High Fidelity ◽  
Proposed Model ◽  
Latent Space ◽  
Wide Range

AbstractShoeprints contain valuable information for tracing evidence in forensic scenes, and they need to be generated into cleaned, sharp, and high-fidelity images. Most of the acquired shoeprints are found with low quality and/or in distorted forms. The high-fidelity shoeprint generation is of great significance in forensic science. A wide range of deep learning models has been suggested for super-resolution, being either generalized approaches or application specific. Considering the crucial challenges in shoeprint based processing and lacking specific algorithms, we proposed a deep learning based GUV-Net model for high-fidelity shoeprint generation. GUV-Net imitates learning features from VAE, U-Net, and GAN network models with special treatment of absent ground truth shoeprints. GUV-Net encodes efficient probabilistic distributions in the latent space and decodes variants of samples together with passed key features. GUV-Net forwards the learned samples to a refinement-unit proceeded to the generation of high-fidelity output. The refinement-unit receives low-level features from the decoding module at distinct levels. Furthermore, the refinement process is made more efficient by inverse-encoded in high dimensional space through a parallel inverse encoding network. The objective functions at different levels enable the model to efficiently optimize the parameters by mapping a low quality image to a high-fidelity one by maintaining salient features which are important to forensics. Finally, the performance of the proposed model is evaluated against state-of-the-art super-resolution network models.

Factors Affecting Molecular Self-Assembly and Its Mechanism

2012 ◽  
Vol 9 (1) ◽  
pp. 43 ◽  
Author(s):  
Hueyling Tan
Keyword(s):  
Self Assembly ◽  
Building Blocks ◽  
Molecular Engineering ◽  
Molecular Structures ◽  
Polymer Science ◽  
New Approach ◽  
Factors Affecting ◽  
Dna Structures ◽  
Self Assembling ◽  
Wide Range

Molecular self-assembly is ubiquitous in nature and has emerged as a new approach to produce new materials in chemistry, engineering, nanotechnology, polymer science and materials. Molecular self-assembly has been attracting increasing interest from the scientific community in recent years due to its importance in understanding biology and a variety of diseases at the molecular level. In the last few years, considerable advances have been made in the use ofpeptides as building blocks to produce biological materials for wide range of applications, including fabricating novel supra-molecular structures and scaffolding for tissue repair. The study ofbiological self-assembly systems represents a significant advancement in molecular engineering and is a rapidly growing scientific and engineering field that crosses the boundaries ofexisting disciplines. Many self-assembling systems are rangefrom bi- andtri-block copolymers to DNA structures as well as simple and complex proteins andpeptides. The ultimate goal is to harness molecular self-assembly such that design andcontrol ofbottom-up processes is achieved thereby enabling exploitation of structures developed at the meso- and macro-scopic scale for the purposes oflife and non-life science applications. Such aspirations can be achievedthrough understanding thefundamental principles behind the selforganisation and self-synthesis processes exhibited by biological systems.

Understanding Conformational Entropy in Small Molecules

2020 ◽  
Author(s):  
Lucian Chan ◽  
Garrett Morris ◽  
Geoffrey Hutchison
Keyword(s):  
Small Molecules ◽  
Degrees Of Freedom ◽  
Absolute Error ◽  
Low Energy ◽  
Standard Entropy ◽  
Free Energies ◽  
Conformational Entropy ◽  
Wide Range ◽  
High Degree ◽  
Empirical Corrections

The calculation of the entropy of flexible molecules can be challenging, since the number of possible conformers grows exponentially with molecule size and many low-energy conformers may be thermally accessible. Different methods have been proposed to approximate the contribution of conformational entropy to the molecular standard entropy, including performing thermochemistry calculations with all possible stable conformations, and developing empirical corrections from experimental data. We have performed conformer sampling on over 120,000 small molecules generating some 12 million conformers, to develop models to predict conformational entropy across a wide range of molecules. Using insight into the nature of conformational disorder, our cross-validated physically-motivated statistical model can outperform common machine learning and deep learning methods, with a mean absolute error ≈4.8 J/mol•K, or under 0.4 kcal/mol at 300 K. Beyond predicting molecular entropies and free energies, the model implies a high degree of correlation between torsions in most molecules, often as- sumed to be independent. While individual dihedral rotations may have low energetic barriers, the shape and chemical functionality of most molecules necessarily correlate their torsional degrees of freedom, and hence restrict the number of low-energy conformations immensely. Our simple models capture these correlations, and advance our understanding of small molecule conformational entropy.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

Extraction of DNA from a Wide Range of Objects by Treatment with Ammonium Salts

2020 ◽  
Vol 36 (6) ◽  
pp. 98-106
Author(s):  
E.I. Levitin ◽  
B.V. Sviridov ◽  
O.V. Piksasova ◽  
T.E. Shustikova
Keyword(s):  
Dna Extraction ◽  
Dna Isolation ◽  
Tissue Samples ◽  
New Approach ◽  
Cell Wall Disruption ◽  
Wide Range ◽  
Low Salt ◽  
Mammalian Blood ◽  
Plasmid Extraction ◽  
Two Hybrid

Currently, simple, rapid, and efficient techniques for DNA isolation from a wide range of organisms are in demand in biotechnology and bioinformatics. A key (and often limiting) step is the cell wall disruption and subsequent DNA extraction from the disintegrated cells. We have developed a new approach to DNA isolation from organisms with robust cell walls. The protocol includes the following steps: treatment of cells or tissue samples with ammonium acetate followed by cell lysis in low-salt buffer with the addition of SDS. Further DNA extraction is carried out according to standard methods. This approach is efficient for high-molecular native DNA isolation from bacteria, ascomycetes, yeast, and mammalian blood; it is also useful for express analysis of environmental microbial isolates and for plasmid extraction for two-hybrid library screening. express method for DNA isolation; ammonium salt treatment (в русских ключевых такой порядок), osmotic breakage of cells This study was financially supported by the NRC "Kurchatov Institute"-GOSNIIGENETIKA Kurchatov Genomic Center.

pH-Dependent Thermal Stability of Vibrio cholerae L-asparaginase

2019 ◽  
Vol 26 (10) ◽  
pp. 743-750 ◽  
Author(s):  
Remya Radha ◽  
Sathyanarayana N. Gummadi
Keyword(s):  
Vibrio Cholerae ◽  
Conformational Changes ◽  
Kinetic Studies ◽  
Structural Features ◽  
Structure Stability ◽  
Kcal Mole ◽  
Scanning Calorimetry ◽  
Wide Range ◽  
Ph Dependent ◽  
Ph Range

Background:pH is one of the decisive macromolecular properties of proteins that significantly affects enzyme structure, stability and reaction rate. Change in pH may protonate or deprotonate the side group of aminoacid residues in the protein, thereby resulting in changes in chemical and structural features. Hence studies on the kinetics of enzyme deactivation by pH are important for assessing the bio-functionality of industrial enzymes. L-asparaginase is one such important enzyme that has potent applications in cancer therapy and food industry.Objective:The objective of the study is to understand and analyze the influence of pH on deactivation and stability of Vibrio cholerae L-asparaginase.Methods:Kinetic studies were conducted to analyze the effect of pH on stability and deactivation of Vibrio cholerae L-asparaginase. Circular Dichroism (CD) and Differential Scanning Calorimetry (DSC) studies have been carried out to understand the pH-dependent conformational changes in the secondary structure of V. cholerae L-asparaginase.Results:The enzyme was found to be least stable at extreme acidic conditions (pH< 4.5) and exhibited a gradual increase in melting temperature from 40 to 81 °C within pH range of 4.0 to 7.0. Thermodynamic properties of protein were estimated and at pH 7.0 the protein exhibited ΔG37of 26.31 kcal mole-1, ΔH of 204.27 kcal mole-1 and ΔS of 574.06 cal mole-1 K-1.Conclusion:The stability and thermodynamic analysis revealed that V. cholerae L-asparaginase was highly stable over a wide range of pH, with the highest stability in the pH range of 5.0–7.0.

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