scholarly journals Interface Refinement of Low-to-Medium Resolution Cryo-EM Complexes using HADDOCK2.4

2021 ◽  
Author(s):  
Tim Neijenhuis ◽  
Siri C. van Keulen ◽  
Alexandre M.J.J. Bonvin
Keyword(s):  
Protein Complexes ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Protein Interfaces ◽  
Density Maps ◽  
Medium Resolution ◽  
Wide Range ◽  
Multimeric Protein

A wide range of cellular processes require the formation of multimeric protein complexes. The rise of cryo-electron microscopy (cryo-EM) has enabled the structural characterization of these protein assemblies. The produced density maps can, however, still suffer from limited resolution, impeding the process of resolving structures at atomic resolution. In order to solve this issue, monomers can be fitted into low-to-medium resolution maps. Unfortunately, the produced models frequently contain atomic clashes at the protein-protein interfaces (PPIs) as intermolecular interactions are typically not considered during monomer fitting. Here, we present a refinement approach based on HADDOCK2.4 to remove intermolecular clashes and optimize PPIs. A dataset of 14 cryo-EM complexes was used to test eight protocols. The best performing protocol, consisting of a semi-flexible simulated annealing refinement with restraints on the centroids of the monomers, was able to decrease intermolecular atomic clashes by 98% without significantly deteriorating the quality of the cryo-EM density fit.

scholarly journals PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps

2016 ◽  
Vol 72 (10) ◽  
pp. 1137-1148 ◽  
Author(s):  
Guray Kuzu ◽  
Ozlem Keskin ◽  
Ruth Nussinov ◽  
Attila Gursoy
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Protein Assemblies ◽  
New Approach ◽  
Cellular Processes ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Crystallographic Structures ◽  
Hiv 1

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

scholarly journals The Calibration Home Base for Imaging Spectrometers

2016 ◽  
Vol 2 ◽  
Author(s):  
Johannes Felix Simon Brachmann ◽  
Andreas Baumgartner ◽  
Peter Gege
Keyword(s):  
Wavelength Range ◽  
Stray Light ◽  
Third Party ◽  
Home Base ◽  
Geometric Calibration ◽  
Wide Range ◽  
Along Track ◽  
Near Future

The Calibration Home Base (CHB) is an optical laboratory designed for the calibration of imaging spectrometers for the VNIR/SWIR wavelength range. Radiometric, spectral and geometric calibration as well as the characterization of sensor signal dependency on polarization are realized in a precise and highly automated fashion. This allows to carry out a wide range of time consuming measurements in an ecient way. The implementation of ISO 9001 standards in all procedures ensures a traceable quality of results. Spectral measurements in the wavelength range 380–1000 nm are performed to a wavelength uncertainty of +- 0.1 nm, while an uncertainty of +-0.2 nm is reached in the wavelength range 1000 – 2500 nm. Geometric measurements are performed at increments of 1.7 µrad across track and 7.6 µrad along track. Radiometric measurements reach an absolute uncertainty of +-3% (k=1). Sensor artifacts, such as caused by stray light will be characterizable and correctable in the near future. For now, the CHB is suitable for the characterization of pushbroom sensors, spectrometers and cameras. However, it is planned to extend the CHBs capabilities in the near future such that snapshot hyperspectral imagers can be characterized as well. The calibration services of the CHB are open to third party customers from research institutes as well as industry.

Artificial protein assemblies with well-defined supramolecular protein nanostructures

2021 ◽  
Author(s):  
Suyeong Han ◽  
Yongwon Jung
Keyword(s):  
Vaccine Development ◽  
De Novo ◽  
Building Blocks ◽  
Protein Assembly ◽  
Protein Assemblies ◽  
Cellular Processes ◽  
Wide Range ◽  
Array Structures ◽  
Small Chemical ◽  
Artificial Protein

Nature uses a wide range of well-defined biomolecular assemblies in diverse cellular processes, where proteins are major building blocks for these supramolecular assemblies. Inspired by their natural counterparts, artificial protein-based assemblies have attracted strong interest as new bio-nanostructures, and strategies to construct ordered protein assemblies have been rapidly expanding. In this review, we provide an overview of very recent studies in the field of artificial protein assemblies, with the particular aim of introducing major assembly methods and unique features of these assemblies. Computational de novo designs were used to build various assemblies with artificial protein building blocks, which are unrelated to natural proteins. Small chemical ligands and metal ions have also been extensively used for strong and bio-orthogonal protein linking. Here, in addition to protein assemblies with well-defined sizes, protein oligomeric and array structures with rather undefined sizes (but with definite repeat protein assembly units) also will be discussed in the context of well-defined protein nanostructures. Lastly, we will introduce multiple examples showing how protein assemblies can be effectively used in various fields such as therapeutics and vaccine development. We believe that structures and functions of artificial protein assemblies will be continuously evolved, particularly according to specific application goals.

scholarly journals Effects of gas–wall interactions on measurements of semivolatile compounds and small polar molecules

2019 ◽  
Vol 12 (6) ◽  
pp. 3137-3149 ◽  
Author(s):  
Xiaoxi Liu ◽  
Benjamin Deming ◽  
Demetrios Pagonis ◽  
Douglas A. Day ◽  
Brett B. Palm ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Transmission Efficiency ◽  
Polar Molecules ◽  
Ionization Mass ◽  
Atmospheric Measurements ◽  
Wide Range ◽  
Teflon Tubing ◽  
Gas Interactions

Abstract. Recent work has quantified the delay times in measurements of volatile organic compounds (VOCs) caused by the partitioning between the gas phase and the surfaces of the inlet tubing and instrument itself. In this study we quantify wall partitioning effects on time responses and transmission of multifunctional, semivolatile, and intermediate-volatility organic compounds (S/IVOCs) with saturation concentrations (C∗) between 100 and 104 µg m−3. The instrument delays of several chemical ionization mass spectrometer (CIMS) instruments increase with decreasing C∗, ranging from seconds to tens of minutes, except for the NO3- CIMS where it is always on the order of seconds. Six different tubing materials were tested. Teflon, including PFA, FEP, and conductive PFA, performs better than metals and Nafion in terms of both delay time and transmission efficiency. Analogous to instrument responses, tubing delays increase as C∗ decreases, from less than a minute to >100 min. The delays caused by Teflon tubing vs. C∗ can be modeled using the simple chromatography model of Pagonis et al. (2017). The model can be used to estimate the equivalent absorbing mass concentration (Cw) of each material, and to estimate delays under different flow rates and tubing dimensions. We also include time delay measurements from a series of small polar organic and inorganic analytes in PFA tubing measured by CIMS. Small polar molecules behave differently than larger organic ones, with their delays being predicted by their Henry's law constants instead of their C∗, suggesting the dominance of partitioning to small amounts of water on sampling surfaces as a result of their polarity and acidity properties. PFA tubing has the best performance for gas-only sampling, while conductive PFA appears very promising for sampling S/IVOCs and particles simultaneously. The observed delays and low transmission both affect the quality of gas quantification, especially when no direct calibration is available. Improvements in sampling and instrument response are needed for fast atmospheric measurements of a wide range of S/IVOCs (e.g., by aircraft or for eddy covariance). These methods and results are also useful for more general characterization of surface–gas interactions.

scholarly journals Atomic-level characterization of protein–protein association

2019 ◽  
Vol 116 (10) ◽  
pp. 4244-4249 ◽  
Author(s):  
Albert C. Pan ◽  
Daniel Jacobson ◽  
Konstantin Yatsenko ◽  
Duluxan Sritharan ◽  
Thomas M. Weinreich ◽  
...  
Keyword(s):  
Structural Information ◽  
Protein Complexes ◽  
Md Simulations ◽  
Atomic Level ◽  
Conformational Ensemble ◽  
Native State ◽  
Protein Interfaces ◽  
Study Association ◽  
Functionally Diverse

Despite the biological importance of protein–protein complexes, determining their structures and association mechanisms remains an outstanding challenge. Here, we report the results of atomic-level simulations in which we observed five protein–protein pairs repeatedly associate to, and dissociate from, their experimentally determined native complexes using a molecular dynamics (MD)–based sampling approach that does not make use of any prior structural information about the complexes. To study association mechanisms, we performed additional, conventional MD simulations, in which we observed numerous spontaneous association events. A shared feature of native association for these five structurally and functionally diverse protein systems was that if the proteins made contact far from the native interface, the native state was reached by dissociation and eventual reassociation near the native interface, rather than by extensive interfacial exploration while the proteins remained in contact. At the transition state (the conformational ensemble from which association to the native complex and dissociation are equally likely), the protein–protein interfaces were still highly hydrated, and no more than 20% of native contacts had formed.

scholarly journals Watching cellular machinery in action, one molecule at a time

2016 ◽  
Vol 216 (1) ◽  
pp. 41-51 ◽  
Author(s):  
Enrico Monachino ◽  
Lisanne M. Spenkelink ◽  
Antoine M. van Oijen
Keyword(s):  
Dynamic Behavior ◽  
Single Molecule ◽  
Protein Complexes ◽  
Imaging Techniques ◽  
Ensemble Averaging ◽  
Cellular Processes ◽  
Cellular Machinery

Single-molecule manipulation and imaging techniques have become important elements of the biologist’s toolkit to gain mechanistic insights into cellular processes. By removing ensemble averaging, single-molecule methods provide unique access to the dynamic behavior of biomolecules. Recently, the use of these approaches has expanded to the study of complex multiprotein systems and has enabled detailed characterization of the behavior of individual molecules inside living cells. In this review, we provide an overview of the various force- and fluorescence-based single-molecule methods with applications both in vitro and in vivo, highlighting these advances by describing their applications in studies on cytoskeletal motors and DNA replication. We also discuss how single-molecule approaches have increased our understanding of the dynamic behavior of complex multiprotein systems. These methods have shown that the behavior of multicomponent protein complexes is highly stochastic and less linear and deterministic than previously thought. Further development of single-molecule tools will help to elucidate the molecular dynamics of these complex systems both inside the cell and in solutions with purified components.

scholarly journals Effects of Gas-Wall Interactions on Measurements of Semivolatile Compounds and Small Polar Molecules

2019 ◽  
Author(s):  
Xiaoxi Liu ◽  
Benjamin Deming ◽  
Demetrios Pagonis ◽  
Douglas A. Day ◽  
Brett B. Palm ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Transmission Efficiency ◽  
Polar Molecules ◽  
Ionization Mass ◽  
Atmospheric Measurements ◽  
Wide Range ◽  
Teflon Tubing ◽  
Gas Interactions

Abstract. Recent work has quantified the delay times in measurements of volatile organic compounds (VOCs) caused by the partitioning between the gas phase and the surfaces of the inlet tubing and instrument itself. In this study we quantify wall partitioning effects on time responses and transmission of multi-functional, semivolatile and intermediate-volatility organic compounds (S/IVOCs) with saturation concentrations (C*) between 100 and 104 µg m−3. The instrument delays of several chemical ionization mass spectrometer (CIMS) instruments increase with decreasing C*, ranging from seconds to tens of minutes, except for the NO3−-CIMS where it is always on the order of seconds. Six different tubing materials were tested. Teflon, including PFA, FEP, and conductive PFA, performs better than metals and Nafion in terms of both delay time and transmission efficiency. Analogous to instrument responses, tubing delays increase as C* decreases, from less than a minute to > 100 min. The delays caused by Teflon tubing vs. C* can be modeled using the simple chromatography model of Pagonis et al. (2017). The model can be used to estimate the equivalent absorbing mass concentration (Cw) of each material, and to estimate delays under different flow rates and tubing dimensions. We also include time delay measurements from a series of small polar organic and inorganic analytes in PFA tubing measured by CIMS. Small polar molecules behave differently than larger organic ones, with their delays being predicted by their Henry’s law constants instead of their C*, suggesting the dominance of partitioning to small amounts of water on sampling surfaces as a result of their polarity and acidity properties. PFA tubing has the best performance for gas-only sampling, while conductive PFA appears very promising for sampling S/IVOCs and particles simultaneously. The observed delays and low transmission both affect the quality of gas quantification, especially when no direct calibration is available. Improvements in sampling and instrument response are needed for fast atmospheric measurements of a wide range of S/IVOCs (e.g., by aircraft or for eddy covariance). These methods and results are also useful for more general characterization of surface/gas interactions.

scholarly journals Back-exchange of deuterium in neutron crystallography: characterization by IR spectroscopy

2017 ◽  
Vol 50 (2) ◽  
pp. 660-664 ◽  
Author(s):  
Ai Woon Yee ◽  
Matthew P. Blakeley ◽  
Martine Moulin ◽  
Michael Haertlein ◽  
Edward Mitchell ◽  
...  
Keyword(s):  
Quality Control ◽  
Ir Spectroscopy ◽  
Scattering Length ◽  
Systematic Method ◽  
Density Maps ◽  
Back Exchange ◽  
Central Facility ◽  
Neutron Crystallography

The application of IR spectroscopy to the characterization and quality control of samples used in neutron crystallography is described. While neutron crystallography is a growing field, the limited availability of neutron beamtime means that there may be a delay between crystallogenesis and data collection. Since essentially all neutron crystallographic work is carried out using D2O-based solvent buffers, a particular concern for these experiments is the possibility of H2O back-exchange across reservoir or capillary sealants. This may limit the quality of neutron scattering length density maps and of the associated analysis. Given the expense of central facility beamtime and the effort that goes into the production of suitably sized (usually perdeuterated) crystals, a systematic method of exploiting IR spectroscopy for the analysis of back-exchange phenomena in the reservoirs used for crystal growth is valuable. Examples are given in which the characterization of D2O/H2O back-exchange in transthyretin crystals is described.

The characterization of volatile molecular substances

1993 ◽  
Vol 443 (1918) ◽  
pp. 313-332 ◽  
Keyword(s):  
Subjective Evaluation ◽  
Sensor Arrays ◽  
Intrinsic Property ◽  
Wide Range ◽  
The Laplace Transform ◽  
Molecular Substances ◽  
Definition Of ◽  
Enclosed Space

Diffusion for gaseous sources comprising more than one type of substance is examined to show how relative concentrations change with time and distance. The large variations which are predicted make nonsense of the popular assumption that odour or smell is an intrinsic property of the source material. However, some characterization of volatile chemical substances is needed. It is shown that this is possible by creating a uniform and stable atmosphere after the relapse of sufficient time by introducing the gas mixture into an enclosed space. In this investigation the situation is analysed for a spherical enclosure using Fourier analysis techniques for the long timescale behaviour and the Laplace transform for the short timescale solution. The measurement of odours via the response of sensor arrays within a spherical enclosure is considered and a proposal is made for utilizing such an enclosure in a definition of volatile molecular substances (analogous to biological ‘smell’). The conditions for optimum compatibility between an array of sensors and a set of calibrands are discussed and the practical means of effecting such measurements are considered in relation to known types of sensor. It is concluded that the quality of volatile molecular substances is definable and measurable down to very low gas concentrations in air: probably below 10 parts per billion for a wide range of gas mixtures unconstrained by such limitations associated with a biological nose such as toxicity, temperature and subjective evaluation.

Emission and Laser-Induced Fluorescence Spectroscopy of Laser-Ablated Titanium Plume

1999 ◽  
Author(s):  
Schubert S. Chu ◽  
Costas P. Grigoropoulos
Keyword(s):  
Time Of Flight ◽  
Laser Induced Fluorescence ◽  
Spectroscopic Techniques ◽  
Wide Range ◽  
Optical Time ◽  
Background Gas ◽  
Spectrally Resolved ◽  
Deposited Film

Abstract Pulsed laser deposition (PLD) of thin films has evolved into a well-recognized technique for a wide range of materials and in a variety of devices. There is great interest in the energy characterization of the ablated plume because this is a key parameter in determining the quality of the deposited film. Spectroscopic techniques, such as optical time-of-flight (TOF,) emission spectroscopy, and laser-induced-fluorescence (LIF) are excellent methods for this purpose since they offer temporal and spatial resolution as well as the capability of distinguishing different species. The effects of laser fluence and background gas pressure on the kinetic energies of the ablated species were found by the optical time-of flight technique and by emission imaging. Furthermore, laser-induced-fluorescence was employed for spectrally resolved imaging. The results provide additional data on the kinetic energy and the distribution of neutral titanium. The axial velocity of neutral titanium was found to be as high as 2 × 104 m/s. The distribution of species within the plume was also determined.

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