scholarly journals Increased usability, algorithmic improvements and incorporation of data mining for structure calculation of proteins with REDCRAFT software package

2020 ◽  
Vol 21 (S9) ◽  
Author(s):  
Casey Cole ◽  
Caleb Parks ◽  
Julian Rachele ◽  
Homayoun Valafar
Keyword(s):  
Nmr Spectroscopy ◽  
Software Package ◽  
Residual Dipolar Couplings ◽  
Protein Structures ◽  
Primary Source ◽  
Structure Calculation ◽  
Resonance Spectroscopy ◽  
Full Potential ◽  
X Ray ◽  
The Impact

Abstract Background Traditional approaches to elucidation of protein structures by Nuclear Magnetic Resonance spectroscopy (NMR) rely on distance restraints also known as Nuclear Overhauser effects (NOEs). The use of NOEs as the primary source of structure determination by NMR spectroscopy is time consuming and expensive. Residual Dipolar Couplings (RDCs) have become an alternate approach for structure calculation by NMR spectroscopy. In previous works, the software package REDCRAFT has been presented as a means of harnessing the information containing in RDCs for structure calculation of proteins. However, to meet its full potential, several improvements to REDCRAFT must be made. Results In this work, we present improvements to REDCRAFT that include increased usability, better interoperability, and a more robust core algorithm. We have demonstrated the impact of the improved core algorithm in the successful folding of the protein 1A1Z with as high as ±4 Hz of added error. The REDCRAFT computed structure from the highly corrupted data exhibited less than 1.0 Å with respect to the X-ray structure. We have also demonstrated the interoperability of REDCRAFT in a few instances including with PDBMine to reduce the amount of required data in successful folding of proteins to unprecedented levels. Here we have demonstrated the successful folding of the protein 1D3Z (to within 2.4 Å of the X-ray structure) using only N-H RDCs from one alignment medium. Conclusions The additional GUI features of REDCRAFT combined with the NEF compliance have significantly increased the flexibility and usability of this software package. The improvements of the core algorithm have substantially improved the robustness of REDCRAFT in utilizing less experimental data both in quality and quantity.

NMR spectroscopy: a multifaceted approach to macromolecular structure

2000 ◽  
Vol 33 (1) ◽  
pp. 29-65 ◽  
Author(s):  
Ann E. Ferentz ◽  
Gerhard Wagner
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Solution Structure ◽  
Residual Dipolar Couplings ◽  
Complete Solution ◽  
Protein Structures ◽  
Sequential Assignment ◽  
Resonance Spectroscopy ◽  
Triple Resonance ◽  
Membrane Bound

1. Introduction 292. Landmarks in NMR of macromolecules 322.1 Protein structures and methods development 322.1.1 Sequential assignment method 322.1.2 Triple-resonance experiments 342.1.3 Structures of large proteins 362.2 Protein–nucleic acid complexes 372.3 RNA structures 382.4 Membrane-bound systems 393. NMR spectroscopy today 403.1 State-of-the-art structure determination 413.2 New methods 443.2.1 Residual dipolar couplings 443.2.2 Direct detection of hydrogen bonds 443.2.3 Spin labeling 453.2.4 Segmental labeling 463.3 Protein complexes 473.4 Mobility studies 503.5 Determination of time-dependent structures 523.6 Drug discovery 534. The future of NMR 544.1 The ease of structure determination 544.2 The ease of making recombinant protein 554.3 Post-translationally modified proteins 554.4 Approaches to large and/or membrane-bound proteins 564.5 NMR in structural genomics 564.6 Synergy of NMR and crystallography in protein structure determination 565. Conclusion 576. Acknowledgements 577. References 57Since the publication of the first complete solution structure of a protein in 1985 (Williamson et al. 1985), tremendous technological advances have brought nuclear magnetic resonance spectroscopy to the forefront of structural biology. Innovations in magnet design, electronics, pulse sequences, data analysis, and computational methods have combined to make NMR an extremely powerful technique for studying biological macromolecules at atomic resolution (Clore & Gronenborn, 1998). Most recently, new labeling and pulse techniques have been developed that push the fundamental line-width limit for resolution in NMR spectroscopy, making it possible to obtain high-field spectra with better resolution than ever before (Dötsch & Wagner, 1998). These methods are facilitating the study of systems of ever-increasing complexity and molecular weight.

scholarly journals REDCRAFT: A Computational Platform Using Residual Dipolar Coupling NMR Data for Determining Structures of Perdeuterated Proteins Without NOEs

2020 ◽  
Author(s):  
Casey A. Cole ◽  
Nourhan S. Daigham ◽  
Gaohua Liu ◽  
Gaetano T. Montelione ◽  
Homayoun Valafar
Keyword(s):  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Software Package ◽  
Residual Dipolar Couplings ◽  
Protein Structures ◽  
Dipolar Couplings ◽  
Large Proteins ◽  
Perdeuterated Proteins ◽  
Small Proteins

AbstractNuclear Magnetic Resonance (NMR) spectroscopy is one of the two primary experimental means of characterizing macromolecular structures, including protein structures. Structure determination by NMR spectroscopy has traditionally relied heavily on distance restraints derived from nuclear Overhauser effect (NOE) measurements. While structure determination of proteins from NOE-based restraints is well understood and broadly used, structure determination by NOEs imposes increasing quantity of data for analysis, increased cost of structure determination and is less available in the study of perdeuterated proteins. In the recent decade, Residual Dipolar Couplings (RDCs) have been investigated as an alternative source of data for structural elucidation of proteins by NMR. Several methods have been reported that utilize RDCs in addition to NOEs, and a few utilize RDC data alone. While these methods have individually demonstrated some successes, none of these methods have exposed the full potential of protein structure determination from RDCs. To date, structure determination of proteins from RDCs is limited to small proteins (less than 8.5 kDa) using RDC data from many alignment media (>3) that cannot be collected from larger proteins. Here we present the latest version of the REDCRAFT software package designed for structure determination of proteins from RDC data alone. We have demonstrated the success of REDCRAFT in structure determination of proteins ranging in size from 50 to 145 residues using experimentally collected data and large proteins (145 to 573 residues) using simulated RDC data that can be collected from perdeuterated proteins. Finally, we demonstrate the accuracy of structure determination of REDCRAFT from RDCs alone in application to the structurally novel PF.2048 protein. The RDC-based structure of PF.2048 exhibited 1.0 Å of BB-RMSD with respect to the NOE-based structure by only using a small amount of backbone RDCs (∼3 restraints per residue) compared to what is required by other approaches.Author SummaryResidual Dipolar Couplings have the potential to reduce the cost and the time needed to characterize protein structures. In addition, RDC data have been demonstrated to concurrently elucidate structure of proteins, perform assignment of resonances, and be used in characterization of the internal dynamics of proteins. Given all the advantages associated with the study of proteins from RDC data, based on the statistics provided by the Protein Databank (PDB), surprisingly the only 124 proteins (out of nearly 150,000 proteins) have utilized RDCs as part of their structure determination. Even a smaller subset of these proteins (approximately 7) have utilized RDCs as the primary source of data for structure determination. The impeding factor in the use of RDCs is the challenging computational and analytical aspects of this source of data. In this report, we demonstrate the success of the REDCRAFT software package in structure determination of proteins using RDC data that can be collected from small and large proteins in a routine fashion. REDCRAFT accomplishes the challenging task of structure determination from RDCs by introducing a unique search and optimization technique that is both robust and computationally tractable. Structure determination from routinely collectable RDC data using REDCRAFT can lead to faster and cheaper study of larger and more complex proteins by NMR spectroscopy in solution state.

Factors affecting the amplitude of the τ angle in proteins: a revisitation

2017 ◽  
Vol 73 (7) ◽  
pp. 618-625 ◽  
Author(s):  
Nicole Balasco ◽  
Luciana Esposito ◽  
Luigi Vitagliano
Keyword(s):  
Protein Structures ◽  
Factors Affecting ◽  
X Ray ◽  
Backbone Conformation ◽  
Potential Factors ◽  
The Stability ◽  
Major Factors ◽  
The Impact ◽  
Open Issues

The protein folded state is the result of the fine balance of a variety of different forces. Even minor structural perturbations may have a significant impact on the stability of these macromolecules. Studies carried out in recent decades have led to the convergent view that proteins are endowed with a flexible spine. One of the open issues related to protein local backbone geometry is the identification of the factors that influence the amplitude of the τ (N—Cα—C) angle. Here, statistical analyses performed on an updated ensemble of X-ray protein structures by dissecting the contribution of the major factors that can potentially influence the local backbone geometry of proteins are reported. The data clearly indicate that the local backbone conformation has a prominent impact on the modulation of the τ angle. Therefore, a proper assessment of the impact of the other potential factors can only be appropriately evaluated when small (φ, ψ) regions are considered. Here, it is shown that when the contribution of the backbone conformation is removed by considering small (φ, ψ) areas, an impact of secondary structure, as defined byDSSP, and/or the residue type on τ is still detectable, although to a limited extent. Indeed, distinct τ-value distributions are detected for Pro/Gly and β-branched (Ile/Val) residues. The key role of the local backbone conformation highlighted here supports the use of variable local backbone geometry in protein refinement protocols.

Imidazole-containing Bispidine Ligands: Synthesis, Structure and Cu(II) Complexation

2011 ◽  
Vol 66 (7) ◽  
pp. 721-728 ◽  
Author(s):  
Martin Walther ◽  
Madlen Matterna ◽  
Stefanie Juran ◽  
Silke Fähnemann ◽  
Holger Stephan ◽  
...  
Keyword(s):  
Solid State ◽  
Nmr Spectroscopy ◽  
Enol Form ◽  
Trans Configuration ◽  
X Ray Diffraction ◽  
X Ray ◽  
The Impact ◽  
Configurational Isomerism

The preparation and characterization of tris-pyridyl bispidine (3,7-diazabicyclo[3.3.1]nonane) derivatives with benzimidazole and imidazole donor groups at the N-3 position of the bispidine skeleton and their copper(II) complexes are reported. The impact of the hetaryl substituents on the configurational isomerism of piperidones and their corresponding bispidones has been studied by NMR spectroscopy, revealing the exclusive appearance in the enol form for the piperidones in solution and the trans-configuration regarding the two pyridyl substituents, as well as the sole formation of the unsymmetric exo-endo isomers for the corresponding bispidones. Thus, the bispidones are preorganized ligands for building pentacoordinated complexes, confirmed by the preparation and characterization of the corresponding Cu(II) complexes. Of the di-pyridyl piperidones with benzimidazole and imidazole substituents, and of the Cu(II) complex of the benzimidazole-containing bispidone, crystals have become available for the analysis by X-ray diffraction, showing that the piperidones form the enol tautomers also in the solid state.

Stereochemistry Determination by Powder X-Ray Diffraction Analysis and NMR Spectroscopy Residual Dipolar Couplings

2009 ◽  
Vol 48 (31) ◽  
pp. 5670-5674 ◽  
Author(s):  
Manuela E. García ◽  
Silvina Pagola ◽  
Armando Navarro-Vázquez ◽  
Damilola D. Phillips ◽  
Chakicherla Gayathri ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Diffraction Analysis ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
X Ray Diffraction ◽  
X Ray

Impact of X-ray induced radiation damage on FD-MAPS of the ARCADIA project

2022 ◽  
Vol 17 (01) ◽  
pp. C01035
Author(s):  
C. Neubüser ◽  
T. Corradino ◽  
S. Mattiazzo ◽  
L. Pancheri
Keyword(s):  
Power Consumption ◽  
Radiation Damage ◽  
High Energy ◽  
Full Potential ◽  
Sensor Design ◽  
Charge Collection Efficiency ◽  
X Ray ◽  
Active Pixel ◽  
Wide Range ◽  
The Impact

Abstract Recent advancements in Monolithic Active Pixel Sensors (MAPS) demonstrated the ability to operate in high radiation environments of up to multiple kGy’s, which increased their appeal as sensors for high-energy physics detectors. The most recent example in such application is the new ALICE inner tracking system, entirely instrumented with CMOS MAPS, that covers an area of about 10 m2. However, the full potential of such devices has not yet been fully exploited, especially in respect of the size of the active area, power consumption, and timing capabilities. The ARCADIA project is developing Fully Depleted (FD) MAPS with an innovative sensor design, that uses a proprietary processing of the backside to improve the charge collection efficiency and timing over a wide range of operational and environmental conditions. The innovative sensor design targets very low power consumption, of the order of 20 mW cm−2 at 100 MHz cm−2 hit flux, to enable air-cooled operations of the sensors. Another key design parameter is the ability to further reduce the power regime of the sensor, down to 5 mW cm−2 or better, for low hit rates like e.g. expected in space experiments. In this contribution, we present a comparison between the detector characteristics predicted with Technology Computer Aided Design (TCAD) simulations and the ones measured experimentally. The comparison focuses on the current-voltage (IV) and capacitance-voltage (CV) characteristics, as well as noise estimated from in-pixel capacitances of passive/active pixel matrices. In view of the targeted applications of this technology, an emphasis is set on the modeling of X-ray induced radiation damage at the Si-SiO2 interface and the impact on the in-pixel sensor capacitance. The so-called new Perugia model has been used in the simulations to predict the sensor performance after total ionizing doses of up to 10 Mrad.

scholarly journals Cryo-EM in drug discovery

2019 ◽  
Vol 47 (1) ◽  
pp. 281-293 ◽  
Author(s):  
Tom Ceska ◽  
Chun-Wa Chung ◽  
Rob Cooke ◽  
Chris Phillips ◽  
Pamela A. Williams
Keyword(s):  
Drug Discovery ◽  
Protein Structures ◽  
Computing Power ◽  
X Ray ◽  
X Ray Crystallography ◽  
The Past ◽  
Ligand Binding Sites ◽  
Phase Plates ◽  
Technological Improvements ◽  
The Impact

Abstract The impact of structural biology on drug discovery is well documented, and the workhorse technique for the past 30 years or so has been X-ray crystallography. With the advent of several technological improvements, including direct electron detectors, automation, better microscope vacuums and lenses, phase plates and improvements in computing power enabled by GPUs, it is now possible to record and analyse images of protein structures containing high-resolution information. This review, from a pharmaceutical perspective, highlights some of the most relevant and interesting protein structures for the pharmaceutical industry and shows examples of how ligand-binding sites, membrane proteins, both big and small, pseudo symmetry and complexes are being addressed by this technique.

scholarly journals Structure Determination by Single-Particle Cryo-Electron Microscopy: Only the Sky (and Intrinsic Disorder) is the Limit

2019 ◽  
Vol 20 (17) ◽  
pp. 4186 ◽  
Author(s):  
Emeka Nwanochie ◽  
Vladimir N. Uversky
Keyword(s):  
Electron Microscopy ◽  
Nmr Spectroscopy ◽  
Structure Determination ◽  
Single Particle ◽  
Protein Structures ◽  
X Ray ◽  
X Ray Crystallography ◽  
Intrinsically Disordered ◽  
Small Proteins ◽  
Cryo Electron Microscopy

Traditionally, X-ray crystallography and NMR spectroscopy represent major workhorses of structural biologists, with the lion share of protein structures reported in protein data bank (PDB) being generated by these powerful techniques. Despite their wide utilization in protein structure determination, these two techniques have logical limitations, with X-ray crystallography being unsuitable for the analysis of highly dynamic structures and with NMR spectroscopy being restricted to the analysis of relatively small proteins. In recent years, we have witnessed an explosive development of the techniques based on Cryo-electron microscopy (Cryo-EM) for structural characterization of biological molecules. In fact, single-particle Cryo-EM is a special niche as it is a technique of choice for the structural analysis of large, structurally heterogeneous, and dynamic complexes. Here, sub-nanometer atomic resolution can be achieved (i.e., resolution below 10 Å) via single-particle imaging of non-crystalline specimens, with accurate 3D reconstruction being generated based on the computational averaging of multiple 2D projection images of the same particle that was frozen rapidly in solution. We provide here a brief overview of single-particle Cryo-EM and show how Cryo-EM has revolutionized structural investigations of membrane proteins. We also show that the presence of intrinsically disordered or flexible regions in a target protein represents one of the major limitations of this promising technique.

Stereochemistry Determination by Powder X-Ray Diffraction Analysis and NMR Spectroscopy Residual Dipolar Couplings

2009 ◽  
Vol 121 (31) ◽  
pp. 5780-5784 ◽  
Author(s):  
Manuela E. García ◽  
Silvina Pagola ◽  
Armando Navarro-Vázquez ◽  
Damilola D. Phillips ◽  
Chakicherla Gayathri ◽  
...  
Keyword(s):  
Nmr Spectroscopy ◽  
Diffraction Analysis ◽  
Residual Dipolar Couplings ◽  
Dipolar Couplings ◽  
X Ray Diffraction ◽  
X Ray

REFINEMENT OF NMR-DETERMINED PROTEIN STRUCTURES WITH DATABASE DERIVED DISTANCE CONSTRAINTS

2005 ◽  
Vol 03 (06) ◽  
pp. 1315-1329 ◽  
Author(s):  
FENG CUI ◽  
ROBERT JERNIGAN ◽  
ZHIJUN WU
Keyword(s):  
Protein Structures ◽  
Rational Drug Design ◽  
Resonance Spectroscopy ◽  
Distance Constraints ◽  
X Ray ◽  
X Ray Crystallography ◽  
Nmr Structures ◽  
High Quality Protein ◽  
Rational Drug ◽  
Distance Data

The protein structures determined by NMR (Nuclear Magnetic Resonance Spectroscopy) are not as detailed and accurate as those by X-ray crystallography and are often underdetermined due to the inadequate distance data available from NMR experiments. The uses of NMR-determined structures in such important applications as homology modeling and rational drug design have thus been severely limited. Here we show that with the increasing numbers of high quality protein structures being determined, a computational approach to enhancing the accuracy of the NMR-determined structures becomes possible by deriving additional distance constraints from the distributions of the distances in databases of known protein structures. We show through a survey on 462 NMR structures that, in fact, many inter-atomic distances in these structures deviate considerably from their database distributions and based on the refinement results on 10 selected NMR structures that these structures can actually be improved significantly when a selected set of distances are constrained within their high probability ranges in their database distributions.

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