Sample From User Collect NMR Data by users Structure Calc. & Display Schedule Set up Experiments Data transfer Maintain Software Instruction Maintain NMRs.

Slides:

Advertisements

Similar presentations

Multipulse techniques

Advertisements

Protein NMR terminology COSY-Correlation spectroscopy Gives experimental details of interaction between hydrogens connected via a covalent bond NOESY-Nuclear.

Continuum of Frequency Excite all Resonances at the same time F

P3- Represent how data flows around a computer system

1 Resonance assignment strategies. 2 Amino acid sequence + The assignment problem.

RTI International RTI International is a trade name of Research Triangle Institute. NMR Hands On UAB Metabolomics Training Course June 02-05,

BIO-PROCESS LAB (B) 2015 KAREN LANCOUR

One-dimensional Spectra Provides 1. Chemical shifts & Relative Intensities 2. J-couplings.

CCPNmr Analysis – from spectrum to structure and more Victoria A. Higman Leibniz-Institut für Molekulare Pharmakologie, Berlin and School of Chemistry,

Incorporating additional types of information in structure calculation: recent advances chemical shift potentials residual dipolar couplings.

Metody szybkiej rejestracji wielowymiarowych widm NMR Wiktor Koźmiński Wydział Chemii Uniwersytetu Warszawskiego.

ABSTRACT: We are interested in determining the conformational changes induced by ligand binding in the intracellular lipid binding protein (iLBP) karitinocyte.

Assignment methods that use heteronuclear shift correlation for larger proteins (>10-15 kD), assignment methods based on 2D homonuclear 1 H- 1 H correlation.

What is an assignment? Associate a given signal back to the originating spin.

4 aromatic protons Can we use 2D to assign this spectrum? Structure first determined by Woodward in 1948 (without NMR!)

Automatic assignment of NMR spectral data from protein sequences using NeuroBayes Slavomira Stefkova, Michal Kreps and Rudolf A Roemer Department of Physics,

NMR Broad Band Spectrometer

How NMR is Used for the Study of Bio-macromolecules Analytical biochemistry Comparative analysis Interactions between biomolecules Structure determination.

Drs. Wei Tian & Yanhui Chen Sep-Dec Main Content Introduction of Nuclear Magnetic Resonance (NMR) Analysis One Dimensional NMRs 1 H NMR 13 C NMR.

NMR Applications in Chemistry

1 Refined Solution Structure of HIV-1 Nef Stephen Grzesiek, Ad Bax, Jin-Shan Hu, Joshua Kaufman, Ira Palmer, Stephen J Stahl, Nico Tjandra and Paul T.

Lab 6. o Do not surf the web o Do not check your unless it’s related to this course o Do not print materials unrelated to lab o Do not connect.

Nuclear Magnetic Resonance in Structural Biology Part I the physical principle the physical principle the spectrometer the spectrometer the NMR spectrum.

How to Analyze of 2D NMR Spectra ( small molecules) 노 정 래.

1 Biomolecular NMR Spectroscopy Methods and applications to proteins Robert Kaptein Novosibirsk, November 2012.

E mag =-μB E:electric field B:magnetic field μ:magnetic moment B B μ μ Low energy(-)High energy(+) μ induced = μ 0 -1 VΧB μ0=awkward constant V=volume.

-1/2 E +1/2 low energy spin state

Biomolecular Nuclear Magnetic Resonance Spectroscopy FROM ASSIGNMENT TO STRUCTURE Sequential resonance assignment strategies NMR data for structure determination.

NANUC Training Course NMRVIEW for Beginners Friday Oct. 11 th, 8am Ryan McKay.

National Magnetic Resonance Facility At Madison NMRFAM

(I) NMR theory and experiments

Lab 4. o Do not surf the web o Do not check your unless it’s related to this course o Do not print materials unrelated to lab o Do not connect.

Protein NMR Part II.

JG/10-09 NMR for structural biology DNA purification Protein domain from a database Protein structure possible since 1980s, due to 2-dimensional (and 3D.

Marcin Płóciennik Poznan Supercomputing and Networking Center OGF23, Barcelona, Spain, June 3rd, 2008 Use case of NMR spectrometry in Virtual Laboratory.

Brendan M. Duggan, Ph.D. Research Interests Applications of NMR Natural products structure elucidation Obtaining structurally useful information Increasing.

Core C-2: NMR Center P.I. C. Allen Bush Director: Bruce Johnson Newly Installed Instrumentation.

1/60 An Iterative Relaxation Technique for the NMR Backbone Assignment Problem Wen-Lian Hsu Institute of Information Science Academia Sinica.

1/62 An Iterative Relaxation Technique for the NMR Backbone Assignment Problem Wen-Lian Hsu Institute of Information Science Academia Sinica.

Nuclear Magnetic Resonance

Strategic Agenda We want to be connected to the internet……… We may even want to host our own web site……… We must have a secure network! What are the.

The Pulse FT NMR Experiment equilibration 90º pulse detection of signals Experiment (t) Data Analysis Fourier Transform Time domain (t)

Claridge Chapter 8. NOE Transient NOEs In standard 1D NOE, one resonance is saturated, and the system must respond to return to equilibrium by the W0.

How NMR is Used for the Study of Biomacromolecules Analytical biochemistry Comparative analysis Interactions between biomolecules Structure determination.

RDCs NMR of Biological Macromolecules in Solution More resonances; shorter T2/broader lines Similar basic techniques- HSQC, TOCSY, NOESY Other experiments.

Tetrahymena telomerase Nhp2p Chin Ju Park January 22, 2008 Progress Reports 6.

Protein NMR IV - Isotopic labeling

NMRbox Data-as-a-Service Overview

Protein NMR Spectroscopy Institute of Biomedical Sciences

SAMPLE SUBMISSION FORM

BIO-PROCESS LAB (B) 2010 KAREN LANCOUR Bio-Process Lab

Calcium-Induced Conformational Switching of Paramecium Calmodulin Provides Evidence for Domain Coupling Jaren et al. Biochemistry 2002, 41,

Get to know SQL Manager SQL Server administration done right

Title: How to determine the solution structure of murine epidermal growth factor by NMR Spectroscopy Hong Liu.

Claridge Chapter 9.

Douglas Kojetin, Ph.D. UC College of Medicine

ILab Accounts If you have not done so already, you must register for an iLab account to use any iLab-controlled instruments and equipment To create an.

Mapping of the Interaction Interface of DNA Polymerase β with XRCC1

Goals of tutorial Introduce NMRbox platform

NMR Spectroscopy – Part 2

1. Pure Protein (0.3 mL, mM; ~ 10 mg)

NMR Spectroscopy Question and Answer Session

Volume 7, Issue 8, Pages (August 1999)

Volume 10, Issue 6, Pages (June 1999)

Structure determination by NMR

Structure determination by NMR

The Arginine-Rich RNA-Binding Motif of HIV-1 Rev Is Intrinsically Disordered and Folds upon RRE Binding Fabio Casu, Brendan M. Duggan, Mirko Hennig

Volume 16, Issue 6, Pages (June 2008)

Proteins Have Too Many Signals!

Volume 110, Issue 11, Pages (June 2016)

Presentation transcript:

Sample From User Collect NMR Data by users Structure Calc. & Display Schedule Set up Experiments Data transfer Maintain Software Instruction Maintain NMRs Develop Methods Train Users How the NMR Lab works currently?

What kinds of high-field NMR we have in IBMS ? Probes : 5mm 1H 5mm probe 1H/19F 5mm probe 1H/Broad band Reverse 5mm probe 1H/15N/13C 5mm probe TXI (1H/13C/31P) 5mm with Z gradient TXI (1H/13C/15N) 5mm with XYZ gradient Probes: 8mm TXI (1H/13C/15N) 8mm with Z gradient Probes: 10mm 1H 10mm probe 1H /19F 10mm probe 1H /Broad band 10mm probe Bruker Avance 600 with XYZ gradient unit (more than 99% used)

Bruker AMX500 with Z gradient unit Probes : 5mm TXI (1H/13C/15N) 5mm with Z gradient (more than 98% used)

Information on web homepage for user’s information Schedule on the web spectrometer reservation Simple Operation Manual step by step instruction Useful Experiments 1D, 2D, 3D, 4D homo-, heteronuclear Parameters setting expt/proc. parameter setting with pp NMR related Software update and short instruction What we have done for NMR users? NMR Experiments Display & Analysis Structure Calc. Data Processing

Examples of Standard Experiments 1D with/without gradient 2D homo with/without gradient COSY, TOCSY, NOESY, ROESY 2D heter HSQC, TROSY, dynamics (T1/T2/NOE/CPMG…) 3D tocsy type TOCSY-HSQC, H(CC)(CO)NH, CC(CO)NH, HCCH-TOCSY 3D noesy type NOESY-HSQC 3D triple resonance for assignment HNCA, HN(CO)CA, HNCO, HN(CA)CO, HNCACB, CBCANH, CBCA(CO)NH, HBHANH, HBHA(CO)NH 3D J-coupling HNHA, HNCA-J, HNHB, HACAHB 4D noesy type 13 C-HMQC-NOESY- 15 N-HSQC Green: available for both AVA600 & AMX500 Black: only available at AVA 600

NMR data processing software XWINNMR (process NMR data on IRIX 6.X & Linux ) License only available for older version nmrPipe (process NMR data on IRIX6.X & Linux) NMR data analysis software AURELIA (analyze NMR data on IRIX 6.X & Linux ) License only available for older version nmrDraw (analyze NMR data on IRIX 6.X & Linux ) nmrView (analyze NMR data on IRIX 6.X & Linux ) Sparky (analyze NMR data on Linux) Example of currently available software

Structure Calculation program and software CSI Chemical Shift Index (making consensus plot on IRIX) TALOS (dihedral angles prediction on IRIX 6.X & Linux ) XPLOR (structure calculation on IRIX) CNS (structure calculation on IRIX6.X & Linux) ARIA (auto NOE assign and structure calculation on IRIX6.X & Linux) Structure display & analysis software INSIGHT II (on IRIX, license from computer center) MOLMOL ( on IRIX & Linux) MOLSCRIPT ( on IRIX) PROCHECK (structure analysis on IRIX) GRASP (on IRIX) VINCE (for making NOE connective plot on IRIX)

NMR dynamics MODELFREE ( on IRIX, Linux & Euler ) NMR data transfer sFTP (with security) ZIP drive (for personal computer) Compact Disk

What will/should be new in the High-field Biomacromolecular Solution NMR core facility? More instruments and probes upgraded AVA500, AVA600, US800s, Cryoprobes More NMR users More new/updated experimental methods for biomacromolecules develop new experiment to fit user’s requirement More software development NMR applications (software manager) New operating service Operators to collect standard experiments Others from your suggestion Thank You!