A Transient and Low-Populated Protein-Folding Intermediate at Atomic Resolution

Science ◽  
2010 ◽  
Vol 329 (5997) ◽  
pp. 1312-1316 ◽  
Author(s):  
Dmitry M. Korzhnev ◽  
Tomasz L. Religa ◽  
Wiktor Banachewicz ◽  
Alan R. Fersht ◽  
Lewis E. Kay
Keyword(s):  
Chemical Shifts ◽  
Relaxation Dispersion ◽  
Atomic Resolution ◽  
General Strategy ◽  
Folding Intermediate ◽  
Carboxyl Terminal ◽  
Resonance Relaxation ◽  
Vector Orientation ◽  
Kinetics Of

Proteins can sample conformational states that are critical for function but are seldom detected directly because of their low occupancies and short lifetimes. In this work, we used chemical shifts and bond-vector orientation constraints obtained from nuclear magnetic resonance relaxation dispersion spectroscopy, in concert with a chemical shift–based method for structure elucidation, to determine an atomic-resolution structure of an “invisible” folding intermediate of a small protein module: the FF domain. The structure reveals non-native elements preventing formation of the native conformation in the carboxyl-terminal part of the protein. This is consistent with the kinetics of folding in which a well-structured intermediate forms rapidly and then rearranges slowly to the native state. The approach introduces a general strategy for structure determination of low-populated and transiently formed protein states.

scholarly journals An RNA dynamic ensemble at atomic resolution

2020 ◽  
Author(s):  
Honglue Shi ◽  
Atul Rangadurai ◽  
Hala Abou Assi ◽  
Rohit Roy ◽  
David A. Case ◽  
...  
Keyword(s):  
Structure Prediction ◽  
Residual Dipolar Couplings ◽  
Chemical Shifts ◽  
3D Structure ◽  
Atomic Resolution ◽  
Data Gap ◽  
Nmr Residual Dipolar Couplings ◽  
And Function ◽  
Dynamic Ensembles

AbstractBiomolecules do not fold into a single 3D structure but rather form dynamic ensembles of many inter-converting conformations1. Knowledge of dynamic ensembles is key for understanding how biomolecules fold and function, and for rationally manipulating their activities in drug discovery and synthetic biology2–4. However, solving dynamic ensembles of biomolecules at atomic resolution is a major challenge in structural biology because the information required to specify the position of all atoms in thousands of conformations in an ensemble far exceeds the information content of experimental measurements. Here we addressed the data gap and dramatically simplified and accelerated RNA ensemble determination by using structure prediction tools that leverage the growing database of RNA structures to generate a conformational library. Library refinement with NMR residual dipolar couplings enabled determination of an atomic-resolution ensemble for HIV-1 TAR as confirmed by quantum-mechanical calculations of NMR chemical shifts, comparison to a crystal structure of a substate, and through the successful redistribution of the ensemble by design using atomic mutagenesis. The ensemble provides an unprecedented view of how bulge residues cooperatively flip out and undergo sugar repuckering to allow the adjoining helices to stack. The generality of this approach will make determination of atomic-resolution RNA ensembles routine.

scholarly journals Slow conformational exchange and overall rocking motion in ubiquitin protein crystals

2017 ◽  
Author(s):  
Vilius Kurauskas ◽  
Sergei A. Izmailov ◽  
Olga N. Rogacheva ◽  
Audrey Hessel ◽  
Isabel Ayala ◽  
...  
Keyword(s):  
Solid State Nmr ◽  
Crystal Packing ◽  
Md Simulations ◽  
Relaxation Dispersion ◽  
Conformational Exchange ◽  
Crystal Forms ◽  
Dispersion Data ◽  
Rocking Motion ◽  
Resonance Relaxation ◽  
Kinetics Of

AbstractProteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, NEar-Rotary-resonance Relaxation Dispersion (NERRD) experiments probe angular backbone motion, while Bloch-McConnell Relaxation Dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with a ∼3-5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.

Determination of microbiological activity during the processing of frost damaged sugar beets

2014 ◽  
pp. 228-231 ◽  
Author(s):  
Maciej Wojtczak ◽  
Aneta Antczak-Chrobot ◽  
Edyta Chmal-Fudali ◽  
Agnieszka Papiewska
Keyword(s):  
Sugar Beet ◽  
Microbiological Activity ◽  
Microbiological Contamination ◽  
Sugar Beets ◽  
Bacterial Metabolites ◽  
Kinetics Of

The aim of the study is to evaluate the kinetics of the synthesis of dextran and other bacterial metabolites as markers of microbiological contamination of sugar beet.

Studies on the Behavior Some Paints in Electro-insulating Fluid Based on Vegetable Esters

2018 ◽  
Vol 69 (5) ◽  
pp. 1139-1144
Author(s):  
Iosif Lingvay ◽  
Adriana Mariana Bors ◽  
Livia Carmen Ungureanu ◽  
Valerica Stanoi ◽  
Traian Rus
Keyword(s):  
Structural Changes ◽  
Oxidation Processes ◽  
High Oleic ◽  
Painting Materials ◽  
Insulating Paper ◽  
Different Types ◽  
Mechanism And Kinetics ◽  
Kinetics Of ◽  
Natural Ester

For the purpose of using three different types of painting materials for the inner protection of the transformer vats, their behavior was studied under actual conditions of operation in the transformer (thermal stress in electro-insulating fluid based on the natural ester in contact with copper for electro-technical use and electro-insulating paper). By comparing determination of the content in furans products (HPLC technique) and gases formed (by gas-chromatography) in the electro-insulating fluid (natural ester with high oleic content) thermally aged at 130 �C to 1000 hours in closed glass vessels, it have been found that the presence the investigated painting materials lead to a change in the mechanism and kinetics of the thermo-oxidation processes. These changes are supported by oxygen dissolved in oil, what leads to decrease both to gases formation CO2, CO, H2, CH4, C2H4 and C2H6) and furans products (5-HMF, 2-FOL, 2 -FAL and 2-ACF). The painting materials investigated during the heat treatment applied did not suffer any remarkable structural changes affecting their functionality in the electro-insulating fluid based on vegetable esters.

Interphase distribution of 2-furylethylenes

1985 ◽  
Vol 50 (8) ◽  
pp. 1642-1647 ◽  
Author(s):  
Štefan Baláž ◽  
Anton Kuchár ◽  
Ernest Šturdík ◽  
Michal Rosenberg ◽  
Ladislav Štibrányi ◽  
...  
Keyword(s):  
Partition Coefficient ◽  
Partition Coefficients ◽  
Transport Rate ◽  
Phase System ◽  
Two Phase ◽  
Interphase Distribution ◽  
Distribution Kinetics ◽  
System 1 ◽  
Kinetics Of

The distribution kinetics of 35 2-furylethylene derivatives in two-phase system 1-octanol-water was investigated. The transport rate parameters in direction water-1-octanol (l1) and backwards (l2) are partition coefficient P = l1/l2 dependent according to equations l1 = logP - log(βP + 1) + const., l2 = -log(βP + 1) + const., const. = -5.600, β = 0.261. Importance of this finding for assesment of distribution of compounds under investigation in biosystems and also the suitability of the presented method for determination of partition coefficients are discussed.

Gradient-Enhanced Inverse-Detected NMR Techniquesfor Determination of 1H-15N Coupling Constants in 2,2-Dimethylpenta-3,4-dienal Derivatives

1997 ◽  
Vol 62 (11) ◽  
pp. 1747-1753 ◽  
Author(s):  
Radek Marek
Keyword(s):  
Double Bond ◽  
Chemical Shifts ◽  
Multiple Bond ◽  
Coupling Constants ◽  
Single Quantum ◽  
Nmr Techniques ◽  
Phase Sensitive ◽  
Heteronuclear Coupling

Determination of 15N chemical shifts and heteronuclear coupling constants of substituted 2,2-dimethylpenta-3,4-dienal hydrazones is presented. The chemical shifts were determined by gradient-enhanced inverse-detected NMR techniques and 1H-15N coupling constants were extracted from phase-sensitive gradient-enhanced single-quantum multiple bond correlation experiments. Stereospecific behaviour of the coupling constants 2J(1H,15N) and 1J(1H,13C) has been used to determine the configuration on a C=N double bond. The above-mentioned compounds exist predominantly as E isomers in deuteriochloroform.

Determination of the Nucleophilicity of Tricarbonyliron Coordinated Cyclohepta-1,3,5-triene

1999 ◽  
Vol 64 (11) ◽  
pp. 1770-1779 ◽  
Author(s):  
Herbert Mayr ◽  
Karl-Heinz Müller
Keyword(s):  
Gibbs Energy ◽  
Ambient Temperature ◽  
Rate Constants ◽  
Second Order ◽  
Order Rate ◽  
Electrophilic Additions ◽  
Kinetics Of

The kinetics of the electrophilic additions of four diarylcarbenium ions (4a-4d) to tricarbonyl(η4-cyclohepta-1,3,5-triene)iron (1) have been studied photometrically. The second-order rate constants match the linear Gibbs energy relationship log k20 °C = s(E + N) and yield the nucleophilicity parameter N(1) = 3.69. It is concluded that electrophiles with E ≥ -9 will react with complex 1 at ambient temperature.

scholarly journals Recognition of hydrogen isotopomers by an open-cage fullerene

2013 ◽  
Vol 371 (1998) ◽  
pp. 20110629 ◽  
Author(s):  
Yasujiro Murata ◽  
Shih-Ching Chuang ◽  
Fumiyuki Tanabe ◽  
Michihisa Murata ◽  
Koichi Komatsu
Keyword(s):  
Equilibrium Constants ◽  
Equilibrium Mixture ◽  
Size Difference ◽  
Binding Affinities ◽  
Kinetic Isotope ◽  
Molecular Sizes ◽  
Lower Temperature ◽  
Kinetics Of ◽  
Pressure Hydrogen

We present our study on the recognition of hydrogen isotopes by an open-cage fullerene through determination of binding affinity of isotopes H 2 /HD/D 2 with the open-cage fullerene and comparison of their relative molecular sizes through kinetic-isotope-release experiments. We took advantage of isotope H 2 /D 2 exchange that generated an equilibrium mixture of H 2 /HD/D 2 in a stainless steel autoclave to conduct high-pressure hydrogen insertion into an open-cage fullerene. The equilibrium constants of three isotopes with the open-cage fullerene were determined at various pressures and temperatures. Our results show a higher equilibrium constant for HD into open-cage fullerene than the other two isotopomers, which is consistent with its dipolar nature. D 2 molecule generally binds stronger than H 2 because of its heavier mass; however, the affinity for H 2 becomes larger than D 2 at lower temperature, when size effect becomes dominant. We further investigated the kinetics of H 2 /HD/D 2 release from open-cage fullerene, proving their relative escaping rates. D 2 was found to be the smallest and H 2 the largest molecule. This notion has not only supported the observed inversion of relative binding affinities between H 2 and D 2 , but also demonstrated that comparison of size difference of single molecules through non-convalent kinetic-isotope effect was applicable.

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