Author Archives: tmaly

Assessment of the Role of 2,2,2-Trifluoroethanol Solvent Dynamics in Inducing Conformational Transitions in Melittin: An Approach with Solvent 19F Low-Field NMR Relaxation and Overhauser Dynamic Nuclear Polarization Studies

Chaubey, Bhawna, Arnab Dey, Abhishek Banerjee, N. Chandrakumar, and Samanwita Pal. “Assessment of the Role of 2,2,2-Trifluoroethanol Solvent Dynamics in Inducing Conformational Transitions in Melittin: An Approach with Solvent 19F Low-Field NMR Relaxation and Overhauser Dynamic Nuclear Polarization Studies.” The Journal of Physical Chemistry B 124, no. 28 (July 16, 2020): 5993–6003.

https://doi.org/10.1021/acs.jpcb.0c03544

2, 2, 2-Trifluoroethanol (TFE) is one of the fluoroalcohols that have been known to induce and stabilize open helical structure in many proteins and peptides. The current study has benchmarked low field 19F NMR relaxation and 19F Overhauser Dynamic Nuclear Polarization (DNP) by providing a brief account of TFE solvent dynamics in a model Melittin (MLT; an antimicrobial peptide) solution with TFE: D2O cosolvent mixture at pH 7.4. Further, this approach has been employed to reveal the solvation of MLT by TFE in a nonbuffered solution with a pH 2.8 for the first time. The structural transition of MLT has been elucidated via solvent dynamics by measuring 19F TFE relaxation rates at 0.34 T for various TFE: D2O compositions in absence (bulk TFE) and in presence of MLT at both the pH values. A complementary initial record of Circular Dichroism (CD) experiments on these aqueous MLT solutions with TFE as cosolvent at two different pH conditions demonstrated the structural transition from random coil to helical, or from folded helical to open helical structure. The molecular correlation time derived from corresponding relaxation rates shows that TFE resides on the MLT surface in both pH conditions. However, the trends in the variation of molecular correlation time ratio as a function of TFE concentration represent that the mechanism and the extent to which TFE affects the MLT structural integrity are different at different pH. The extraction of the DNP coupling parameter from steady state 19F ODNP experiments performed in presence of TEMPOL at 0.34 T revealed changes in solvation dynamics of TFE concomitant with MLT structural transition. In summary, 19F relaxation and ODNP measurements made at low field have allowed direct monitoring of TFE dynamics during MLTs structural transition in terms of preferential solvation. The choice of experiments performed at moderately low field (0.34 T) enabled us to exploit on the one hand almost 1200-fold mitigation of the strong contribution of 19F CSA at 11.76 T, while on the other hand the ODNP experiment offered a window for probing molecular dynamics on timescales of the order of 10-1000 picoseconds.

[NMR] 4th webinar of the Early Career Researcher

Dear Colleagues,

The 4th webinar of the Early Career Researcher version of ICMRBS series will take place on Wednesday the 16th December 2020, 12 p.m. PST3 p.m. EDT 8 p.m. GMT 9 p.m. CET /1:30 a.m. IST (India- 17th Dec)/4 a.m. CST (China- 17th Dec) /7 a.m. ADET (Australia- 17th Dec)Please note that the webinar this month has been moved to a different time again to accommodate the speakers from 3 different continents! May I please emphasise again our interest to include ECR speakers from all over the World so wherever you are, if you have an interesting story to tell, please come forward and contact one of our committee.

In this webinar, the three scientific talks on the theme of “Solid State NMR” will be delivered by:
Dr Lauriane Lecoq– CNRS (Lyon, France): The hepatitis B virus capsid seen by solid-state NMR
Dr Marc Sani-The University of Melbourne (Melbourne, Australia): Spin labelled peptide for in-cell DNP solid-state NMR
Asst Prof Andrew Nieuwkoop-Rutgers University (New Jersey, USA): Impacts of protein deuteration and MAS rate on 1H-13C solid-state distance measurements

And for our non-scientific session this month, we are delighted to have Prof Arthur Palmer (Columbia University, USA) who will be sharing his career journey with us. The title of his talk is:Your career from A to Z: Learning from my mistakes

The Zoom link is as below: https://uqz.zoom.us/j/86322867824?pwd=Z015YWdOcHBFVmRmSXZZOEpENUgrZz09

Passcode: ICMRBSECR
Hope to see you all there!

Regards,
Karol

On behalf of the ICMRBS ECR committee
Visit our Website and follow us on Twitter and Instagram!

Contact us to present your work!!!

Angelo Gallo (A.Gallo.1@warwick.ac.uk
Karoline Sanches (karolsanches@gmail.com
Nick Fowler (n.j.fowler@sheffield.ac.uk
Reid Alderson (reid.alderson@utoronto.ca)
Yanni Chin (y.chin@uq.edu.au)

Karoline Sanches Mestre em Biofísica Molecular 
Departamento de Física  Instituto de Biociências, Letras e Ciências Exatas – IBILCE/UNESPSão José do Rio Preto – SP(017)991443193
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[NMR] Ampere Biological Solid-State NMR School

AMPERE Biological Solid-State NMR School

Online Phase: January 13, 2021 – May 26, 2021

Combined Attendance/Online Week:

Berlin, 14.06. -18.06.2021

MDC.C, AXON 1, Robert-Rössle-Str. 10, 13125 Berlin

Dear biological solid-state NMR enthusiast, we will have our biannual Ampere Biological Solid-State NMR School again in 2021! It will be a bipartite course, with an online school of basics from January to May 2021, and a scientific get-together in June 2021. Registration for combined virtual and real event is 40 €, including AMPERE membership. Depending on the situation, the workshop in Berlin will be held under distance-enforcing conditions and participant attendance may be limited to 40 persons. The workshop is geared towards the exchange of experience and nitty-gritty experimental details as well as for networking among PhD students and postdocs. The lectures will be transmitted for those who cannot travel. Students are strongly encouraged to present a poster, but it is of course not required for participation since the course is also designed for newcomers in biological solid-state NMR.

The program features introductory lectures twice a month on Wednesdays from 15:00 to 16:00. There will be a 60 minutes presentation and 15 minutes for the discussion/question session, as well as exercises supplied. Afterwards virtual poster presentations of two participants will take place, 10 mins presentation, 10 mins discussion. In the following week, the exercises on the topic of the lecture will be discussed, again on Wednesdays, 15:00, and solutions presented.

All attendees agree to join the conference dinner on Wednesday, June 16, either in person or via the web. Tables will be arranged outdoors in Berlin and online.

Registration

Please send an email to: steuer@fmp-berlin.de . This should include the full name, affiliation (full address) and in case you would like to present a poster, send the title. You will receive a request for payment after confirmation of registration. Places are limited.

Program (detailed version under: https://biosolidnmr-school.org/)

13.01              Quantum Mechanics Beat Meier
20.01              Exercises Quantum Mechanics
27.01              Anisotropic Interactions and MAS Beat Meier
03.02              Exercises Anisotropic Interactions
10.02               Time-Dependent Hamiltonians Matthias Ernst
17.02               Exercises Time-Dependent Hamiltonians
24.02               Solving Time-Dependent Hamiltonians Matthias Ernst
03.03              Exercises Solving Time-Dependent Hamiltonians
10.03              Linewidths Basics/Relaxation Beat Meier
17.03              Exercises Linewidths Basics
30./31.03        Product Operator Calculations for Biochemists Hartmut Oschkinat
07.04              SIMPSON Thomas Vosegaard
14.04              Exercises SIMPSON
21.04               Introduction into EPR Enrica Bordignon
28.04              Exercises EPR
05.05               Dynamic Nuclear Polarisation Bob Griffin  
12.05              Exercises Dynamic Nuclear Polarisation
19.05              The Challenges of Modern Structural Biology Huub de Groot
26.05              Installation of CCPN Vicky Higman/Anja Böckmann

Combined Attendance/Online Week:

The lecture slots are 1h30, except for Friday afternoon, some include exercises and sometimes lectures are 2×45 mins, with a separate exercise section.

Sunday13.06.21Monday14.06.21Tuesday15.06.21Wednesday16.06.21Thursday17.06.21Friday18.06.21
9:00-10:30Decouplin/
Recoupling Theory  Ernst
Carbon Detection/Assignments/CCPN Böckmann/MeierThe Spectrometer/Probes  EngelkeDNP   GriffinStructure Calculation Basics  Bardiaux/Higman
10:30-11:00 Coffee Coffee Coffee Coffee Coffee
11:00-12:30Decoupling/Recoupling    VosegaardProton Detection & Fast MAS  Meier/BöckmannSample Prep Bacteria/ Cell-free Böckmann/OschkinatIntegrative Ensemble Calculations Bonomi Structure   Oschkinat/Meier
12:30-14:00 Lunch Lunch Lunch Lunch Lunch
14:00-15:30Exercises   Ernst/VosegaardAssignment Procedures/CCPN  Böckmann//HigmanRelaxation/Dynamics  ReifStudentsPoster Talks(online)Low Populated StatesJensenEPR in Structural BiologyBordignon
15:30-16:00 Coffee Coffee Coffee  In cell MAS NMR Baldus
16:00-17:30Pulse Sequences  PolenovaExercises  Polenova/MeierIntegrative Structural Biology A. LangeStudents Poster Talks(online) 
17:30-18:00 WelcomeMixer(outdoors)QuestionsQuestions (30 mins)Students Poster TalksConference Dinner (outdoors)Questions (online) 

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School-Conference “Spinus”

Dear colleagues,
Please, help us to disseminate information:

Welcome to the 18th International School-Conference “Spinus-2021. Magnetic Resonance and its Applications” organized by the Saint
Petersburg State University from March 29 to April 2, 2021. This time
the conference will be held online format (via ZOOM) due to
limitations of the COVID-19 epidemic. The goal of “Spinus” is to
provide to young scientists a platform for discussion of the use of
all aspects of magnetic resonance methods and techniques, as well as
computational and theoretical approaches, for the solving of
fundamental and applied problems in physics, chemistry, medicine and biology. The official language of the “Spinus” is English.
The scope of the “Spinus” Conference includes the following topics:
  Modern trends in NMR, ESR and NQR
  Magnetic resonance for fundamental science
  Magnetic resonance imaging
  Computer Modeling
  NMR in the Earth magnetic field
  Magnetic resonance for industry
  Related areas
Extended abstracts will be published in the Book of Proceedings.
Selected papers of participants will be published in a special issue
of the journal “Applied Magnetic Resonance”.

More information and applications for “Spinus 2021” are available on the website  http://spinus.spb.ru

Vladimir Chizhik
Professor
Scientific adviser of the School-Conference “Spinus”

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Diffusion measurements with continuous hydrogenation in PHIP

Bussandri, S., L. Buljubasich, and R.H. Acosta. “Diffusion Measurements with Continuous Hydrogenation in PHIP.” Journal of Magnetic Resonance 320 (November 2020): 106833.

https://doi.org/10.1016/j.jmr.2020.106833.

DOSY is a powerful spectroscopic NMR technique that resolves components in mixtures through the evaluation of different diffusion coefficients. The application of DOSY to dilute mixtures is hampered by the low signal to noise ratios (SNR), leading to long acquisition times. The use of PHIP may resolve this issue as long as reproducible signals are obtained in order to perform 2D experiments. Here we show that the use of hollow membranes and adequate gas flow produce constant polarization for a time-span that enables the acquisition of 2D experiments. A pressure gradient is evidenced by the presence of convection, which is accounted for by using a DPGSE sequence. The influence of J-coupling evolution during the sequence is studied both numerically and experimentally, to determine the optimum echo-time. The applicability of the method for samples with poor SNR is explored by setting the reaction rate to achieve a low intensity of polarized signals.

SQUID-based ultralow-field MRI of a hyperpolarized material using signal amplification by reversible exchange

Lee, Seong-Joo, Keunhong Jeong, Jeong Hyun Shim, Hyun Joon Lee, Sein Min, Heelim Chae, Sung Keon Namgoong, and Kiwoong Kim. “SQUID-Based Ultralow-Field MRI of a Hyperpolarized Material Using Signal Amplification by Reversible Exchange.” Scientific Reports 9, no. 1 (December 2019): 12422.

https://doi.org/10.1038/s41598-019-48827-5

The signal amplification by reversible exchange (SABRE) technique is a very promising method for increasing magnetic resonance (MR) signals. SABRE can play a particularly large role in studies with a low or ultralow magnetic field because they suffer from a low signal-to-noise ratio. In this work, we conducted real-time superconducting quantum interference device (SQUID)-based nuclear magnetic resonance (NMR)/magnetic resonance imaging (MRI) studies in a microtesla-range magnetic field using the SABRE technique after designing a bubble-separated phantom. A maximum enhancement of 2658 for 1H was obtained for pyridine in the SABRE-NMR experiment. A clear SABRE-enhanced MR image of the bubble-separated phantom, in which the para-hydrogen gas was bubbling at only the margin, was successfully obtained at 34.3 μT. The results show that SABRE can be successfully incorporated into an ultralow-field MRI system, which enables new SQUID-based MRI applications. SABRE can shorten the MRI operation time by more than 6 orders of magnitude and establish a firm basis for future low-field MRI applications.

[NMR] Postdoctoral position – DNP – Debelouchina lab – UCSD

Postdoctoral position – Debelouchina lab

UCSDSensitivity-enhanced NMR spectroscopy in cells

The Debelouchina lab at UCSD has an NIH-funded position for a postdoctoral researcher to work on the development of in-cell DNP methodologies and applications. Candidates should have expertise in biomolecular solid-state NMR spectroscopy or solid-state NMR/DNP methodology development, and interest in learning chemical biology and cell biology techniques. The project will be supported by a dedicated 600 MHz DNP NMR spectrometer equipped with 1.9 mm and 3.2 mm low temperature probes. In addition, UCSD has outstanding resources for magnetic resonance spectroscopy including 900 MHz, 750 MHz, and 2 x 700 MHz solid-state NMR spectrometers; 800 MHz, 600 MHz and 500 MHz solution NMR spectrometers; and an X-band EPR spectrometer. UCSD and the San Diego area offer numerous opportunities for networking and collaboration with other NMR spectroscopy, cryo-EM, cryo-ET, imaging, synthetic chemistry and biology groups. Candidates should send a cover letter, CV and the names of three references to gdebelouchina@UCSD.EDU
For more information, take a look at our website and publications:
http://debelouchinalab.ucsd.edu/
https://pubmed.ncbi.nlm.nih.gov/31746101/
https://pubmed.ncbi.nlm.nih.gov/30845353/

___________________________
Galia Debelouchina, Ph.D.
Assistant Professor
she/her
Department of Chemistry and Biochemistry
University of California, San Diego
9500 Gilman Drive
La Jolla, CA 92093

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Scalable dissolution-dynamic nuclear polarization with rapid transfer of a polarized solid #DNPNMR

Kouřil, Karel, Hana Kouřilová, Samuel Bartram, Malcolm H. Levitt, and Benno Meier. “Scalable Dissolution-Dynamic Nuclear Polarization with Rapid Transfer of a Polarized Solid.” Nature Communications 10, no. 1 (December 2019): 1733.

https://doi.org/10.1038/s41467-019-09726-5

In dissolution-dynamic nuclear polarization, nuclear spins are hyperpolarized at cryogenic temperatures using radicals and microwave irradiation. The hyperpolarized solid is dissolved with hot solvent and the solution is transferred to a secondary magnet where strongly enhanced magnetic resonance signals are observed. Here we present a method for transferring the hyperpolarized solid. A bullet containing the frozen, hyperpolarized sample is ejected using pressurized helium gas, and shot into a receiving structure in the secondary magnet, where the bullet is retained and the polarized solid is dissolved rapidly. The transfer takes approximately 70 ms. A solenoid, wound along the entire transfer path ensures adiabatic transfer and limits radical-induced low-field relaxation. The method is fast and scalable towards small volumes suitable for high-resolution nuclear magnetic resonance spectroscopy while maintaining high concentrations of the target molecule. Polarization levels of approximately 30% have been observed for 1-13C-labelled pyruvic acid in solution.

Lignin-polysaccharide interactions in plant secondary cell walls revealed by solid-state NMR #DNPNMR

Kang, Xue, Alex Kirui, Malitha C. Dickwella Widanage, Frederic Mentink-Vigier, Daniel J. Cosgrove, and Tuo Wang. “Lignin-Polysaccharide Interactions in Plant Secondary Cell Walls Revealed by Solid-State NMR.” Nature Communications 10, no. 1 (December 2019): 347.

https://doi.org/10.1038/s41467-018-08252-0

Lignin is a complex aromatic biopolymer that strengthens and waterproofs plant secondary cell walls, enabling mechanical stability in trees and long-distance water transport in xylem. Lignin removal is a key step in paper production and biomass conversion to biofuels, motivating efforts to re-engineer lignin biosynthesis. However, the physical nature of lignin’s interactions with wall polysaccharides is not well understood. Here we show that lignin selfaggregates to form highly hydrophobic and dynamically unique nanodomains, with extensive surface contacts to xylan. Solid-state NMR spectroscopy of intact maize stems, supported by dynamic nuclear polarization, reveals that lignin has abundant electrostatic interactions with the polar motifs of xylan. Lignin preferentially binds xylans with 3-fold or distorted 2-fold helical screw conformations, indicative of xylans not closely associated with cellulose. These findings advance our knowledge of the molecular-level organization of lignocellulosic biomass, providing the structural foundation for optimization of post-harvest processing for biofuels and biomaterials.

[NMR] Postdoctoral position @NHMFL

A postdoctoral position is available from Feburary 2021 for solid-state NMR at the National High Magnetic Field Laboratory (NHMFL) in Tallahassee, Florida. This postdoc will support the operation and development of the 36T/1.5GHz Series-Connected-Hybrid (SCH) NMR program for material and biological applications. The NHMFL has a wide array of state-of-art NMR instruments from 600 MHz to 1.5 GHz including the 36 T SCH magnet and a 600 MHz MAS DNP system. The NMR/MRI program has an active and stimulating research and development environment with a number of staff scientists and engineers. This postdoc will have opportunities and support for independent and collaborative research.

Minimum qualifications include a Ph.D. in Chemistry, Physics, Biology or a related discipline. To apply, please send a CV, a cover letter describing your experience and research interests, and contact information for three references to

Zhehong Gan (gan@magnet.fsu.edu) or Robert Schruko (schurko@magnet.fsu.edu)
National High Magnetic Field Laboratory
1800 E. Paul Dirac Dr., Tallahassee, FL 32310, USA

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