Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

2012 ◽  
Vol 40 (5) ◽  
pp. 1014-1020 ◽  
Author(s):  
Kamil Tamiola ◽  
Frans A.A. Mulder
Keyword(s):  
Structural Information ◽  
Chemical Shifts ◽  
Disordered Proteins ◽  
Photoactive Yellow Protein ◽  
Structural Protein ◽  
Online Tool ◽  
Order And Disorder ◽  
Aggregation Behaviour ◽  
Shift Analysis ◽  
Chemical Shift Analysis

NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are available and idiosyncratic sensitivity of backbone chemical shifts to structural information is treated in a sensible manner. In the present paper, we describe methods to detect structural protein changes from chemical shifts, and present an online tool [ncSPC (neighbour-corrected Structural Propensity Calculator)], which unites aspects of several current approaches. Examples of structural propensity calculations are given for two well-characterized systems, namely the binding of α-synuclein to micelles and light activation of photoactive yellow protein. These examples spotlight the great power of NMR chemical shift analysis for the quantitative assessment of protein disorder at the atomic level, and further our understanding of biologically important problems.

scholarly journals Aromaticities of Five Membered Heterocycles through Dimethyldihydropyrenes Probe by Magnetic and Geometric Criteria

2015 ◽  
Vol 2015 ◽  
pp. 1-11
Author(s):  
Maria ◽  
Khurshid Ayub
Keyword(s):  
Chemical Shifts ◽  
Reference Models ◽  
H Nmr ◽  
Quantitative Estimates ◽  
Shift Analysis ◽  
Structural Criterion ◽  
Stabilization Energies ◽  
Suitable Reference ◽  
Chemical Shift Analysis ◽  
Aromatic Stabilization

Aromaticities of five membered heterocycles, containing up to three heteroatoms, are quantified through the dimethyldihydropyrene (DHP) probe. Bond fixation caused by the fusion of heterocycles to the dimethyldihydropyrene nucleus (DHPN) was measured by changes in the1H NMR chemical shifts (magnetic) and bond lengths alterations (structural criterion). Chemical shifts of dihydropyrenes were calculated at GIAO HF/6-31G(d)//B3LYP/6-31+G(d). For1H NMR chemical shift analysis, two nonaromatic reference models are studied. Among the studied heterocycles, pyrazole and triazole are about 80–85% aromatic relative to benzene, through both magnetic and geometric criteria. Thiazole and oxazoles are found least aromatic where quantitative estimates of aromaticities are about 34–42%, relative to benzene. These quantitative estimates of aromaticities of five membered heterocycles are also comparable to those from aromatic stabilization energies. The quantification of aromaticity through energetic, magnetic, and structural criteria can deliver the similar inferences provided that suitable reference systems are chosen.

Chemical-shift analysis of O Kα by EPMA color-mapping method for BiSrCaCuO superconductive specimen

1992 ◽  
Vol 50 (1) ◽  
pp. 82-83
Author(s):  
H. Takahashi ◽  
T. Okumura ◽  
Y. Seo ◽  
A. Kabaya ◽  
C. Nielsen
Keyword(s):  
Chemical Shift ◽  
Crystal Structures ◽  
Chemical Shifts ◽  
Mapping Method ◽  
Color Mapping ◽  
Shift Analysis ◽  
Spectral Peaks ◽  
Sintering Method ◽  
Chemical Shift Analysis ◽  
Acid Phthalate

The chemical shifts of x-ray spectra are now frequently observed with EPMA (Electron Probe Microanalysis). The conventional method of chemical-shift analysis with EPMA is to compare the peak shapes and peak positions of standard spectra with those of unknown spectra. We reported that O-Kα peak shapes detected by using a TAP (Thallium acid phthalate) crystal reflect their crystal structures. Fig. 1 shows these O-Kα spectral peaks. In the present study, concerning the BiSrCaCuO superconductor made by the sintering method, it was observed that the O-Kα spectra of several kinds of phases reflected their crystal structures. Moreover, it is now possible to observe these chemical shifts of spectra by using the color mapping method in EPMA.

scholarly journals Understanding 125Te NMR chemical shifts in disymmetric organo-telluride compounds from natural chemical shift analysis

2020 ◽  
Vol 22 (4) ◽  
pp. 2319-2326 ◽  
Author(s):  
Ewa Pietrasiak ◽  
Christopher P. Gordon ◽  
Christophe Copéret ◽  
Antonio Togni
Keyword(s):  
Chemical Shift ◽  
Chemical Shifts ◽  
Lone Pair ◽  
Magnetic Coupling ◽  
Nmr Chemical Shifts ◽  
Shift Analysis ◽  
Theoretical Investigations ◽  
Chemical Shift Analysis

Magnetic coupling of the lone pair: theoretical investigations reveal the origin of 125Te chemical shift in disymmetric organotellurides

Mathematical and Computational Techniques for Drug Discovery: Promises and Developments

2019 ◽  
Vol 18 (32) ◽  
pp. 2774-2799 ◽  
Author(s):  
Krishnan Balasubramanian
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Quantum Chemical ◽  
Intrinsically Disordered Proteins ◽  
Hepatitis Virus ◽  
Disordered Proteins ◽  
Computational Techniques ◽  
Large Set ◽  
Structural Protein ◽  
Intrinsically Disordered

We review various mathematical and computational techniques for drug discovery exemplifying some recent works pertinent to group theory of nested structures of relevance to phylogeny, topological, computational and combinatorial methods for drug discovery for multiple viral infections. We have reviewed techniques from topology, combinatorics, graph theory and knot theory that facilitate topological and mathematical characterizations of protein-protein interactions, molecular-target interactions, proteomics, genomics and statistical data reduction procedures for a large set of starting chemicals in drug discovery. We have provided an overview of group theoretical techniques pertinent to phylogeny, protein dynamics especially in intrinsically disordered proteins, DNA base permutations and related algorithms. We consider computational techniques derived from high level quantum chemical computations such as QM/MM ONIOM methods, quantum chemical optimization of geometries complexes, and molecular dynamics methods for providing insights into protein-drug interactions. We have considered complexes pertinent to Hepatitis Virus C non-structural protein 5B polymerase receptor binding of C5-Arylidebne rhodanines, complexes of synthetic potential vaccine molecules with dengue virus (DENV) and HIV-1 virus as examples of various simulation studies that exemplify the utility of computational tools. It is demonstrated that these combinatorial and computational techniques in conjunction with experiments can provide promising new insights into drug discovery. These techniques also demonstrate the need to consider a new multiple site or allosteric binding approach to drug discovery, as these studies reveal the existence of multiple binding sites.

scholarly journals Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation

2019 ◽  
Vol 116 (41) ◽  
pp. 20446-20452 ◽  
Author(s):  
Utsab R. Shrestha ◽  
Puneet Juneja ◽  
Qiu Zhang ◽  
Viswanathan Gurumoorthy ◽  
Jose M. Borreguero ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Intrinsically Disordered Protein ◽  
Physical Models ◽  
Dynamics Simulation ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Eukaryotic Proteomes ◽  
Heterogeneous Ensemble

Intrinsically disordered proteins (IDPs) are abundant in eukaryotic proteomes, play a major role in cell signaling, and are associated with human diseases. To understand IDP function it is critical to determine their configurational ensemble, i.e., the collection of 3-dimensional structures they adopt, and this remains an immense challenge in structural biology. Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. Here, by employing enhanced sampling MD we reproduce the experimental small-angle neutron and X-ray scattering profiles and the NMR chemical shifts of the disordered N terminal (SH4UD) of c-Src kinase without reweighting or constraining the simulations. The unbiased simulation results reveal a weakly funneled and rugged free energy landscape of SH4UD, which gives rise to a heterogeneous ensemble of structures that cannot be described by simple polymer theory. SH4UD adopts transient helices, which are found away from known phosphorylation sites and could play a key role in the stabilization of structural regions necessary for phosphorylation. Our findings indicate that adequately sampled molecular simulations can be performed to provide accurate physical models of flexible biosystems, thus rationalizing their biological function.

scholarly journals Disorder in a two-domain neuronal Ca2+-binding protein regulates domain stability and dynamics using ligand mimicry

2020 ◽  
Author(s):  
Lasse Staby ◽  
Katherine R. Kemplen ◽  
Amelie Stein ◽  
Michael Ploug ◽  
Jane Clarke ◽  
...  
Keyword(s):  
Intrinsically Disordered Proteins ◽  
Three Dimensional ◽  
Life Time ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Order And Disorder ◽  
C Terminus ◽  
Close Relationship ◽  
Stability Dynamics ◽  
And Function

Abstract Understanding the interplay between sequence, structure and function of proteins has been complicated in recent years by the discovery of intrinsically disordered proteins (IDPs), which perform biological functions in the absence of a well-defined three-dimensional fold. Disordered protein sequences account for roughly 30% of the human proteome and in many proteins, disordered and ordered domains coexist. However, few studies have assessed how either feature affects the properties of the other. In this study, we examine the role of a disordered tail in the overall properties of the two-domain, calcium-sensing protein neuronal calcium sensor 1 (NCS-1). We show that loss of just six of the 190 residues at the flexible C-terminus is sufficient to severely affect stability, dynamics, and folding behavior of both ordered domains. We identify specific hydrophobic contacts mediated by the disordered tail that may be responsible for stabilizing the distal N-terminal domain. Moreover, sequence analyses indicate the presence of an LSL-motif in the tail that acts as a mimic of native ligands critical to the observed order–disorder communication. Removing the disordered tail leads to a shorter life-time of the ligand-bound complex likely originating from the observed destabilization. This close relationship between order and disorder may have important implications for how investigations into mixed systems are designed and opens up a novel avenue of drug targeting exploiting this type of behavior.

scholarly journals Neural Upscaling from Residue-Level Protein Structure Networks to Atomistic Structures

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1788
Author(s):  
Vy T. Duong ◽  
Elizabeth M. Diessner ◽  
Gianmarc Grazioli ◽  
Rachel W. Martin ◽  
Carter T. Butts
Keyword(s):  
Protein Structure ◽  
Intrinsically Disordered Proteins ◽  
Dynamic Models ◽  
Structural Information ◽  
Coarse Graining ◽  
Molecular Structures ◽  
Disordered Proteins ◽  
Intrinsically Disordered ◽  
Scalable Network ◽  
Atomic Coordinates

Coarse-graining is a powerful tool for extending the reach of dynamic models of proteins and other biological macromolecules. Topological coarse-graining, in which biomolecules or sets thereof are represented via graph structures, is a particularly useful way of obtaining highly compressed representations of molecular structures, and simulations operating via such representations can achieve substantial computational savings. A drawback of coarse-graining, however, is the loss of atomistic detail—an effect that is especially acute for topological representations such as protein structure networks (PSNs). Here, we introduce an approach based on a combination of machine learning and physically-guided refinement for inferring atomic coordinates from PSNs. This “neural upscaling” procedure exploits the constraints implied by PSNs on possible configurations, as well as differences in the likelihood of observing different configurations with the same PSN. Using a 1 μs atomistic molecular dynamics trajectory of Aβ1–40, we show that neural upscaling is able to effectively recapitulate detailed structural information for intrinsically disordered proteins, being particularly successful in recovering features such as transient secondary structure. These results suggest that scalable network-based models for protein structure and dynamics may be used in settings where atomistic detail is desired, with upscaling employed to impute atomic coordinates from PSNs.

scholarly journals Random coil chemical shifts for serine, threonine and tyrosine phosphorylation over a broad pH range

2019 ◽  
Vol 73 (12) ◽  
pp. 713-725 ◽  
Author(s):  
Ruth Hendus-Altenburger ◽  
Catarina B. Fernandes ◽  
Katrine Bugge ◽  
Micha B. A. Kunze ◽  
Wouter Boomsma ◽  
...  
Keyword(s):  
Chemical Shift ◽  
Secondary Structure ◽  
Intrinsically Disordered Proteins ◽  
Chemical Shifts ◽  
Random Coil ◽  
Disordered Proteins ◽  
Phosphoryl Group ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Secondary Chemical

Abstract Phosphorylation is one of the main regulators of cellular signaling typically occurring in flexible parts of folded proteins and in intrinsically disordered regions. It can have distinct effects on the chemical environment as well as on the structural properties near the modification site. Secondary chemical shift analysis is the main NMR method for detection of transiently formed secondary structure in intrinsically disordered proteins (IDPs) and the reliability of the analysis depends on an appropriate choice of random coil model. Random coil chemical shifts and sequence correction factors were previously determined for an Ac-QQXQQ-NH2-peptide series with X being any of the 20 common amino acids. However, a matching dataset on the phosphorylated states has so far only been incompletely determined or determined only at a single pH value. Here we extend the database by the addition of the random coil chemical shifts of the phosphorylated states of serine, threonine and tyrosine measured over a range of pH values covering the pKas of the phosphates and at several temperatures (www.bio.ku.dk/sbinlab/randomcoil). The combined results allow for accurate random coil chemical shift determination of phosphorylated regions at any pH and temperature, minimizing systematic biases of the secondary chemical shifts. Comparison of chemical shifts using random coil sets with and without inclusion of the phosphoryl group, revealed under/over estimations of helicity of up to 33%. The expanded set of random coil values will improve the reliability in detection and quantification of transient secondary structure in phosphorylation-modified IDPs.

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