NMR Resonance Assignment Assisted by Mass Spectrometry

Size: px
Start display at page:

Download "NMR Resonance Assignment Assisted by Mass Spectrometry"

Transcription

1 NMR Resonance Assignment Assisted by Mass Spectrometry This lecture talked about a NMR resonance assignment assisted by mass spectrometry [1, 2]. 1 Motivation Nuclear magnetic resonance (NMR) provides a useful tool for the structural determination of biomollecules, especially for those molecules that are difficult to crystallize for diffraction studies. During the structure determination by NMR, a key step is the resonance assignment of chemical shifts. The traditional NMR resonance assignment is to use the triple resonance experiments, such as HNCA, to help identify the connectivities between amino acids. However, for some proteins that are difficult to express in doubly labelled forms, we may need the structure determination strategies that depend on only the basic 1 H 15 N HSQC experiment, which requires only 15 N isotopic labelling. In [1, 2], a new approach by integration of NMR and mass spectrometry (MS) is considered for protein resonance assignment. 2 Mass Spectrometry Assisted NMR Assignment 2.1 Principle of the Approach The MS-assisted NMR assignment approach relies on the fact that both NMR and MS are able to monitor rates of exchange of amide protons (HX rate) in water deuterons. Based on this observation, we can connect crosspeaks in NMR data and fragment masses in MS data by correlating the HX rates to help the sequential assignment. 2.2 Extracting HX Rates by HSQC The processes of extracting HX rates by HSQC are shown in Figure 1(a). We can extract the amide exchange rates by monitoring the loss of individual 1

2 cross-peak intensities as a function of of time after dissolving a protein in the deuterated water, i.e., I(t) = I 0 (exp( kt) + const), where k is the residuespecific HX rate. Figure 1(b) shows an example of the loss of cross-peak intensities after dissolving the protein ubiquitin in the deuterated water for certain time. Figure 1: Extracting HX rates by HSQC [1]. 2.3 Extracting HX Rates by MS The procedures of extracting HX rates by MS are described in Figure 2(a). The HX rate measured at each time point is decided by the difference between the centroid of the isotopic peak cluster for the deuterated sample and the centroid of the undeuterated reference. Figure 2(b) shows an example of mass increase after deuterium incorporation. 2.4 Correlating HX rates between NMR and MS The time courses of the exchange from NMR data is calculated by summing the distributions expected for each amino acid. More precisely, the the deuteron distribution d(t) is computed by 2

3 Figure 2: Extracting HX rates by MS. 1, if half-life of the amide H/D exchange is shorted than 1min; d(t) = 0, if half-life of the amide H/D exchange is longer than 1 week; 1 exp( kt), otherwise. where k is the amide proton exchange rate and t is the time interval for exchange. In order to correlate HX rates from NMR and MS, we first plot the time courses of exchange D(t) = n i=1 1 exp( k it), where n is the number of data points in a fragment. After that, we superimpose experimental points from the MS data. A correlation example of deuterium incorporation between the NMR and MS data is shown in Figure MS Assisted Assignment The following generate-and-test procedure is used in [1] to demonstrate how MS helps NMR resonance assignment: (1) Perform an a priori NMR assignment. 3

4 Figure 3: The correlation of deuterium incorporation between the NMR and MS data. (2) Predict the exchange data for all residues from HSQC. (3) Compare the exchange data from HSQC with the data from MS. (4) Score the comparison by function score = exp( (D expt D calc ) 2 /(nσ 2 )), where n is the number of data points, and D expt and D calc are deuterium levels from the MS experiment data and the calculation from the NMR data. Figure 4 shows an example of sequential assignment scores for protein ubiquitin. 3 MS Assisted NMR Assignment in Reductively 1 3C-Methylated Proteins The approach depends on different rates of reductive methylation at each primary amine site. After we run NMR and MS experiments, we can obtain normalized percentages of 13 C incorporation from HSQC and MS data, as shown Figure 5. The NMR peak assignment can be performed by comparing the NMR and MS percentages of 13 C incorporation, as illustrated in Figure 6. 4

5 Figure 4: The sequential assignment scores for protein ubiquitin. References [1] L. Feng, R. Orlando, and J.H. Prestegard. Mass spectrometry assisted assignment of NMR resonances in 15N labeled proteins. J. AM. Chem. Soc., 126, , [2] Megan A. Macnaughtan, Austin M. Kane, and James H. Prestegard. Mass Spectrometry Assisted Assignment of NMR Resonances in C13 Reductively 13C-Methylated Proteins. J. AM. Chem. Soc., 127 (50), ,

6 Figure 5: The normalized percentages of 13 C incorporation. Figure 6: The assignment of NMR peaks (The 5:1 sample means that the molar ratio of 13 C-formaldehyde to primary amine in the sample is 5 : 1). 6

BMB/Bi/Ch 173 Winter 2018

BMB/Bi/Ch 173 Winter 2018 BMB/Bi/Ch 173 Winter 2018 Homework Set 8.1 (100 Points) Assigned 2-27-18, due 3-6-18 by 10:30 a.m. TA: Rachael Kuintzle. Office hours: SFL 220, Friday 3/2 4:00-5:00pm and SFL 229, Monday 3/5 4:00-5:30pm.

More information

BMB/Bi/Ch 173 Winter 2018

BMB/Bi/Ch 173 Winter 2018 BMB/Bi/Ch 173 Winter 2018 Homework Set 8.1 (100 Points) Assigned 2-27-18, due 3-6-18 by 10:30 a.m. TA: Rachael Kuintzle. Office hours: SFL 220, Friday 3/2 4-5pm and SFL 229, Monday 3/5 4-5:30pm. 1. NMR

More information

Intermediates Detection and Hydrogen Exchange

Intermediates Detection and Hydrogen Exchange Intermediates Detection and Hydrogen Exchange NMR methods for detecting intermediates and excited states Amide exchange Methods for detecting Amide Exchange Application of Amide Exchange to proteins NMR

More information

Longitudinal-relaxation enhanced fast-pulsing techniques: New tools for biomolecular NMR spectroscopy

Longitudinal-relaxation enhanced fast-pulsing techniques: New tools for biomolecular NMR spectroscopy Longitudinal-relaxation enhanced fast-pulsing techniques: New tools for biomolecular NMR spectroscopy Bernhard Brutscher Laboratoire de Résonance Magnétique Nucléaire Institut de Biologie Structurale -

More information

Sequential Assignment Strategies in Proteins

Sequential Assignment Strategies in Proteins Sequential Assignment Strategies in Proteins NMR assignments in order to determine a structure by traditional, NOE-based 1 H- 1 H distance-based methods, the chemical shifts of the individual 1 H nuclei

More information

Using NMR to study Macromolecular Interactions. John Gross, BP204A UCSF. Nov 27, 2017

Using NMR to study Macromolecular Interactions. John Gross, BP204A UCSF. Nov 27, 2017 Using NMR to study Macromolecular Interactions John Gross, BP204A UCSF Nov 27, 2017 Outline Review of basic NMR experiment Multidimensional NMR Monitoring ligand binding Structure Determination Review:

More information

SUPPLEMENTARY INFORMATION

SUPPLEMENTARY INFORMATION Parallel Allostery by camp and PDE Coordinates Activation and Termination Phases in camp Signaling Srinath Krishnamurthy, 1 Nikhil Kumar Tulsian, 1 Arun Chandramohan, 1 and Ganesh S. Anand 1, * 1 Department

More information

Biochemistry 530 NMR Theory and Practice. Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington

Biochemistry 530 NMR Theory and Practice. Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington Biochemistry 530 NMR Theory and Practice Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington 1D spectra contain structural information.. but is hard to extract:

More information

Supporting Information for: A. Portz 1, C. R. Gebhardt 2, and M. Dürr 1, Giessen, D Giessen, Germany

Supporting Information for: A. Portz 1, C. R. Gebhardt 2, and M. Dürr 1, Giessen, D Giessen, Germany Supporting Information for: Real-time Investigation of the H/D Exchange Kinetics of Porphyrins and Oligopeptides by means of Neutral Cluster Induced Desorption/Ionization Mass Spectrometry A. Portz 1,

More information

Christopher Pavlik Bioanalytical Chemistry March 2, 2011

Christopher Pavlik Bioanalytical Chemistry March 2, 2011 Nuclear Magnetic Resonance of Proteins Christopher Pavlik Bioanalytical Chemistry March 2, 2011 Nuclear Magnetic Resonance NMR Application of a magnetic field causes absorption of EM energy that induces

More information

Protein NMR. Bin Huang

Protein NMR. Bin Huang Protein NMR Bin Huang Introduction NMR and X-ray crystallography are the only two techniques for obtain three-dimentional structure information of protein in atomic level. NMR is the only technique for

More information

Protein Structure Determination using NMR Spectroscopy. Cesar Trinidad

Protein Structure Determination using NMR Spectroscopy. Cesar Trinidad Protein Structure Determination using NMR Spectroscopy Cesar Trinidad Introduction Protein NMR Involves the analysis and calculation of data collected from multiple NMR techniques Utilizes Nuclear Magnetic

More information

Acta Crystallographica Section D

Acta Crystallographica Section D Supporting information Acta Crystallographica Section D Volume 70 (2014) Supporting information for article: Structural basis of the heterodimerization of the MST and RASSF SARAH domains in the Hippo signalling

More information

Molecular Modeling lecture 2

Molecular Modeling lecture 2 Molecular Modeling 2018 -- lecture 2 Topics 1. Secondary structure 3. Sequence similarity and homology 2. Secondary structure prediction 4. Where do protein structures come from? X-ray crystallography

More information

Introduction solution NMR

Introduction solution NMR 2 NMR journey Introduction solution NMR Alexandre Bonvin Bijvoet Center for Biomolecular Research with thanks to Dr. Klaartje Houben EMBO Global Exchange course, IHEP, Beijing April 28 - May 5, 20 3 Topics

More information

Nuclear Magnetic Resonance Spectroscopy (NMR)

Nuclear Magnetic Resonance Spectroscopy (NMR) OCR Chemistry A 432 Spectroscopy (NMR) What is it? An instrumental method that gives very detailed structural information about molecules. It can tell us - how many of certain types of atom a molecule

More information

Effects of Chemical Exchange on NMR Spectra

Effects of Chemical Exchange on NMR Spectra Effects of Chemical Exchange on NMR Spectra Chemical exchange refers to any process in which a nucleus exchanges between two or more environments in which its NMR parameters (e.g. chemical shift, scalar

More information

- Basic understandings: - Mapping interactions:

- Basic understandings: - Mapping interactions: NMR-lecture April 6th, 2009, FMP Berlin Outline: Christian Freund - Basic understandings: Relaxation Chemical exchange - Mapping interactions: -Chemical shift mapping (fast exchange) Linewidth analysis

More information

Biochemistry 530 NMR Theory and Practice

Biochemistry 530 NMR Theory and Practice Biochemistry 530 NMR Theory and Practice Gabriele Varani Department of Biochemistry and Department of Chemistry University of Washington 1D spectra contain structural information.. but is hard to extract:

More information

NMR in Structural Biology

NMR in Structural Biology NMR in Structural Biology Exercise session 2 1. a. List 3 NMR observables that report on structure. b. Also indicate whether the information they give is short/medium or long-range, or perhaps all three?

More information

Name: BCMB/CHEM 8190, BIOMOLECULAR NMR FINAL EXAM-5/5/10

Name: BCMB/CHEM 8190, BIOMOLECULAR NMR FINAL EXAM-5/5/10 Name: BCMB/CHEM 8190, BIOMOLECULAR NMR FINAL EXAM-5/5/10 Instructions: This is an open book, limited time, exam. You may use notes you have from class and any text book you find useful. You may also use

More information

Electronic Supplementary Information for Sulfur, Oxygen, and Nitrogen Mustards: Stability and Reactivity

Electronic Supplementary Information for Sulfur, Oxygen, and Nitrogen Mustards: Stability and Reactivity Electronic Supplementary Information for Sulfur, Oxygen, and Nitrogen Mustards: Stability and Reactivity Contents Qi-Qiang Wang, Rowshan Ara Begum, Victor W. Day, Kristin Bowman-James* Department of Chemistry,

More information

Kinetic Isotope Effects

Kinetic Isotope Effects 1 Experiment 31 Kinetic Isotope Effects Isotopic substitution is a useful technique for the probing of reaction mechanisms. The change of an isotope may affect the reaction rate in a number of ways, providing

More information

Protein dynamics from NMR Relaxation data

Protein dynamics from NMR Relaxation data Protein dynamics from NMR Relaxation data Clubb 3/15/17 (S f2 ) ( e ) Nitrogen-15 relaxation ZZ-exchange R 1 = 1/T 1 Longitudinal relaxation (decay back to z-axis) R 2 = 1/T 2 Spin-spin relaxation (dephasing

More information

NMR in Medicine and Biology

NMR in Medicine and Biology NMR in Medicine and Biology http://en.wikipedia.org/wiki/nmr_spectroscopy MRI- Magnetic Resonance Imaging (water) In-vivo spectroscopy (metabolites) Solid-state t NMR (large structures) t Solution NMR

More information

Timescales of Protein Dynamics

Timescales of Protein Dynamics Timescales of Protein Dynamics From Henzler-Wildman and Kern, Nature 2007 Dynamics from NMR Show spies Amide Nitrogen Spies Report On Conformational Dynamics Amide Hydrogen Transverse Relaxation Ensemble

More information

PROTEIN NMR SPECTROSCOPY

PROTEIN NMR SPECTROSCOPY List of Figures List of Tables xvii xxvi 1. NMR SPECTROSCOPY 1 1.1 Introduction to NMR Spectroscopy 2 1.2 One Dimensional NMR Spectroscopy 3 1.2.1 Classical Description of NMR Spectroscopy 3 1.2.2 Nuclear

More information

Protein Structure Analysis and Verification. Course S Basics for Biosystems of the Cell exercise work. Maija Nevala, BIO, 67485U 16.1.

Protein Structure Analysis and Verification. Course S Basics for Biosystems of the Cell exercise work. Maija Nevala, BIO, 67485U 16.1. Protein Structure Analysis and Verification Course S-114.2500 Basics for Biosystems of the Cell exercise work Maija Nevala, BIO, 67485U 16.1.2008 1. Preface When faced with an unknown protein, scientists

More information

Lecture 11. IR Theory. Next Class: Lecture Problem 4 due Thin-Layer Chromatography

Lecture 11. IR Theory. Next Class: Lecture Problem 4 due Thin-Layer Chromatography Lecture 11 IR Theory Next Class: Lecture Problem 4 due Thin-Layer Chromatography This Week In Lab: Ch 6: Procedures 2 & 3 Procedure 4 (outside of lab) Next Week in Lab: Ch 7: PreLab Due Quiz 4 Ch 5 Final

More information

Experimental Techniques in Protein Structure Determination

Experimental Techniques in Protein Structure Determination Experimental Techniques in Protein Structure Determination Homayoun Valafar Department of Computer Science and Engineering, USC Two Main Experimental Methods X-Ray crystallography Nuclear Magnetic Resonance

More information

LineShapeKin NMR Line Shape Analysis Software for Studies of Protein-Ligand Interaction Kinetics

LineShapeKin NMR Line Shape Analysis Software for Studies of Protein-Ligand Interaction Kinetics LineShapeKin NMR Line Shape Analysis Software for Studies of Protein-Ligand Interaction Kinetics http://lineshapekin.net Spectral intensity Evgenii L. Kovrigin Department of Biochemistry, Medical College

More information

Protein NMR. Part III. (let s start by reviewing some of the things we have learned already)

Protein NMR. Part III. (let s start by reviewing some of the things we have learned already) Protein NMR Part III (let s start by reviewing some of the things we have learned already) 1. Magnetization Transfer Magnetization transfer through space > NOE Magnetization transfer through bonds > J-coupling

More information

CHEM 241 UNIT 5: PART A DETERMINATION OF ORGANIC STRUCTURES BY SPECTROSCOPIC METHODS [MASS SPECTROMETRY]

CHEM 241 UNIT 5: PART A DETERMINATION OF ORGANIC STRUCTURES BY SPECTROSCOPIC METHODS [MASS SPECTROMETRY] CHEM 241 UNIT 5: PART A DETERMINATION OF ORGANIC STRUCTURES BY SPECTROSCOPIC METHODS [MASS SPECTROMETRY] 1 Introduction Outline Mass spectrometry (MS) 2 INTRODUCTION The analysis of the outcome of a reaction

More information

Experiment 11: NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

Experiment 11: NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY Experiment 11: NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY Purpose: This is an exercise to introduce the use of nuclear magnetic resonance spectroscopy, in conjunction with infrared spectroscopy, to determine

More information

Timescales of Protein Dynamics

Timescales of Protein Dynamics Timescales of Protein Dynamics From Henzler-Wildman and Kern, Nature 2007 Summary of 1D Experiment time domain data Fourier Transform (FT) frequency domain data or Transverse Relaxation Ensemble of Nuclear

More information

Assignment 3 Due Tuesday, March 31, 2009

Assignment 3 Due Tuesday, March 31, 2009 Assignment 3 Due Tuesday, March 31, 2009 Download and read the Math_techniques.pdf file from the Handouts section of the class web page. Do problems 1, 2, and 4 following section C (for problem 1, you

More information

In a solution, there are thousands of atoms generating magnetic fields, all in random directions.

In a solution, there are thousands of atoms generating magnetic fields, all in random directions. Nuclear Magnetic Resonance Spectroscopy: Purpose: onnectivity, Map of - framework Process: In nuclear magnetic resonance spectroscopy, we are studying nuclei. onsider this circle to represent a nucleus

More information

Protein Dynamics Relaxation techniques

Protein Dynamics Relaxation techniques Protein Dynamics Relaxation techniques Daniel Mathieu Bruker Users Meeting 2016, Karlsruhe Innovation with Integrity Proteins aren t exactly rock solid 10.11.2016 Users meeting 2016 2 Characterizing Dynamic

More information

Chapter 6. The interaction of Src SH2 with the focal adhesion kinase catalytic domain studied by NMR

Chapter 6. The interaction of Src SH2 with the focal adhesion kinase catalytic domain studied by NMR The interaction of Src SH2 with the focal adhesion kinase catalytic domain studied by NMR 103 Abstract The interaction of the Src SH2 domain with the catalytic domain of FAK, including the Y397 SH2 domain

More information

1. 3-hour Open book exam. No discussion among yourselves.

1. 3-hour Open book exam. No discussion among yourselves. Lecture 13 Review 1. 3-hour Open book exam. No discussion among yourselves. 2. Simple calculations. 3. Terminologies. 4. Decriptive questions. 5. Analyze a pulse program using density matrix approach (omonuclear

More information

3D NMR 3D NMR 3D NMR. Visualising 3D NMR spectra. strip plots. preparation mixing mixing t1 t2 t3 I S T I

3D NMR 3D NMR 3D NMR. Visualising 3D NMR spectra. strip plots. preparation mixing mixing t1 t2 t3 I S T I 3D NMR 3D NMR Chris Waudby c.waudby@ucl.ac.uk 3D NMR Visualising 3D NMR spectra preparation mixing mixing t1 t2 t3 I S T I 2 indirect dimensions, independently incremented evolution times Much longer acquisition

More information

Useful background reading

Useful background reading Overview of lecture * General comment on peptide bond * Discussion of backbone dihedral angles * Discussion of Ramachandran plots * Description of helix types. * Description of structures * NMR patterns

More information

COSY type experiments exploring through-bond homonuclear correlations

COSY type experiments exploring through-bond homonuclear correlations COSY type experiments exploring through-bond homonuclear correlations Assistant Professor Kenneth Kongstad Bioanalytical Chemistry and Metabolomics Research Group Section for Natural Products and Peptides

More information

Hour Examination # 4

Hour Examination # 4 CHEM 346 Organic Chemistry I Fall 2014 Exam # 4 Solutions Key Page 1 of 12 CHEM 346 Organic Chemistry I Fall 2014 Instructor: Paul Bracher Hour Examination # 4 Wednesday, December 3 rd, 2014 6:00 8:00

More information

Residual Dipolar Couplings BCMB/CHEM 8190

Residual Dipolar Couplings BCMB/CHEM 8190 Residual Dipolar Couplings BCMB/CHEM 8190 Recent Reviews Prestegard, A-Hashimi & Tolman, Quart. Reviews Biophys. 33, 371-424 (2000). Bax, Kontaxis & Tjandra, Methods in Enzymology, 339, 127-174 (2001)

More information

Look for absorption bands in decreasing order of importance:

Look for absorption bands in decreasing order of importance: 1. Match the following to their IR spectra (30 points) Look for absorption bands in decreasing order of importance: a e a 2941 1716 d f b 3333 c b 1466 1.the - absorption(s) between 3100 and 2850 cm-1.

More information

Supplemental Information

Supplemental Information Supplemental Information Neutralizing positive charges at the surface of a protein lowers its rate of amide hydrogen exchange without altering its structure or increasing its thermostability. Bryan F.

More information

T 1, T 2, NOE (reminder)

T 1, T 2, NOE (reminder) T 1, T 2, NOE (reminder) T 1 is the time constant for longitudinal relaxation - the process of re-establishing the Boltzmann distribution of the energy level populations of the system following perturbation

More information

Supplemental data for

Supplemental data for Supplemental data for A Real-Time Guanine Nucleotide Exchange Assay using NMR: Activation of RhoA by PDZ- RhoGEF. Geneviève M.C. Gasmi-Seabrook 1,3, Christopher B. Marshall 1,3, Melissa Cheung 1,3, Bryan

More information

Nuclear Magnetic Resonance Spectroscopy: Purpose: Connectivity, Map of C-H framework

Nuclear Magnetic Resonance Spectroscopy: Purpose: Connectivity, Map of C-H framework Nuclear Magnetic Resonance Spectroscopy: Purpose: Connectivity, Map of C- framework Four Factors of Proton NMR (PMR OR NMR):. Symmetry: Number of chemically different protons (symmetry) as shown by number

More information

HSQC spectra for three proteins

HSQC spectra for three proteins HSQC spectra for three proteins SH3 domain from Abp1p Kinase domain from EphB2 apo Calmodulin What do the spectra tell you about the three proteins? HSQC spectra for three proteins Small protein Big protein

More information

NMR BMB 173 Lecture 16, February

NMR BMB 173 Lecture 16, February NMR The Structural Biology Continuum Today s lecture: NMR Lots of slides adapted from Levitt, Spin Dynamics; Creighton, Proteins; And Andy Rawlinson There are three types of particles in the universe Quarks

More information

Triple Resonance Experiments For Proteins

Triple Resonance Experiments For Proteins Triple Resonance Experiments For Proteins Limitations of homonuclear ( 1 H) experiments for proteins -the utility of homonuclear methods drops quickly with mass (~10 kda) -severe spectral degeneracy -decreased

More information

ZAHID IQBAL WARRAICH

ZAHID IQBAL WARRAICH Q1 Chromatography is an important analytical technique in chemistry. There is a number of techniques under the general heading of chromatography. (a) Paper and gas chromatography rely on partition to separate

More information

1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI )

1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI ) Uses of NMR: 1) NMR is a method of chemical analysis. (Who uses NMR in this way?) 2) NMR is used as a method for medical imaging. (called MRI ) 3) NMR is used as a method for determining of protein, DNA,

More information

Coupling of Functional Hydrogen Bonds in Pyridoxal-5 -phosphate- Enzyme Model Systems Observed by Solid State NMR

Coupling of Functional Hydrogen Bonds in Pyridoxal-5 -phosphate- Enzyme Model Systems Observed by Solid State NMR Supporting Information for Coupling of Functional ydrogen Bonds in Pyridoxal-5 -phosphate- Enzyme Model Systems bserved by Solid State NMR Shasad Sharif, David Schagen, Michael D. Toney, and ans-einrich

More information

BCMB / CHEM 8190 Biomolecular NMR GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE

BCMB / CHEM 8190 Biomolecular NMR GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE BCMB / CHEM 8190 Biomolecular NMR GRADUATE COURSE OFFERING IN NUCLEAR MAGNETIC RESONANCE "Biomolecular Nuclear Magnetic Resonance" is a course intended for all graduate students with an interest in applications

More information

INTRODUCTORY CHEMISTRY FOR WATER QUALITY TECHNOLOGY I. Chemistry 11 and Principles of Mathematics 12 is strongly recommended.

INTRODUCTORY CHEMISTRY FOR WATER QUALITY TECHNOLOGY I. Chemistry 11 and Principles of Mathematics 12 is strongly recommended. CHEMISTRY 115 INTRODUCTORY CHEMISTRY FOR WATER QUALITY TECHNOLOGY I Prerequisites: Format: Chemistry 11 and Principles of Mathematics 12 is strongly recommended. 4 hours lecture + 3 hours lab per week

More information

Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS

Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS Supporting Protocol This protocol describes the construction and the force-field parameters of the non-standard residue for the Ag + -site using CNS CNS input file generatemetal.inp: remarks file generate/generatemetal.inp

More information

Structurele Biologie NMR

Structurele Biologie NMR MR journey Structurele Biologie MR 5 /3C 3 /65 MR & Structural biology course setup lectures - Sprangers R & Kay LE ature (27) basics of MR (Klaartje ouben: k.houben@uu.nl; 4/2) from peaks to data (ans

More information

ion mobility spectrometry IR spectroscopy

ion mobility spectrometry IR spectroscopy Debasmita Gho 29.10.2016 Introducti on Owing to its accuracy, sensitivity, and speed, mass spectrometry (MS) coupled to fragmentation techniques is the method of choice for determining the primary structure

More information

The lecture schedule is only a rough guide and will be likely changed as needed.

The lecture schedule is only a rough guide and will be likely changed as needed. CEHM 239 ORGANIC CHEMISTRY II Spring 2010 Instructor: Professor Hyun-Soon Chong Chemistry Division, BCPS Dept, IIT, LS 398, Chong@iit.edu, 312-567-3235 Course Hours: TR 1:50pm-3:05pm in LS 111 Office Hours:

More information

Inorganic Spectroscopic and Structural Methods

Inorganic Spectroscopic and Structural Methods Inorganic Spectroscopic and Structural Methods Electromagnetic spectrum has enormous range of energies. Wide variety of techniques based on absorption of energy e.g. ESR and NMR: radiowaves (MHz) IR vibrations

More information

NMR parameters intensity chemical shift coupling constants 1D 1 H spectra of nucleic acids and proteins

NMR parameters intensity chemical shift coupling constants 1D 1 H spectra of nucleic acids and proteins Lecture #2 M230 NMR parameters intensity chemical shift coupling constants Juli Feigon 1D 1 H spectra of nucleic acids and proteins NMR Parameters A. Intensity (area) 1D NMR spectrum: integrated intensity

More information

The rest of topic 11 INTRODUCTION TO ORGANIC SPECTROSCOPY

The rest of topic 11 INTRODUCTION TO ORGANIC SPECTROSCOPY The rest of topic 11 INTRODUCTION TO ORGANIC SPECTROSCOPY 1. Mass spectrometry: SPECTROSCOPIC TECHNIQUES - A technique capable of identifying the presence of various mass segments of organic molecules.

More information

Deuteration: Structural Studies of Larger Proteins

Deuteration: Structural Studies of Larger Proteins Deuteration: Structural Studies of Larger Proteins Problems with larger proteins Impact of deuteration on relaxation rates Approaches to structure determination Practical aspects of producing deuterated

More information

Nature Structural & Molecular Biology: doi: /nsmb.3194

Nature Structural & Molecular Biology: doi: /nsmb.3194 Supplementary Figure 1 Mass spectrometry and solution NMR data for -syn samples used in this study. (a) Matrix-assisted laser-desorption and ionization time-of-flight (MALDI-TOF) mass spectrum of uniformly-

More information

Chemistry Organic Chemistry II, Spring 2018

Chemistry Organic Chemistry II, Spring 2018 Chemistry 2320 Organic Chemistry II, Spring 2018 Instructor: Dr. Tom Chang Office: Widtsoe 337 Phone: 797-3545 Email: tom.chang@usu.edu Meeting Time/Place: MWF 10:30-11:20 am, Eccles Business Building

More information

In a solution, there are thousands of atoms generating magnetic fields, all in random directions.

In a solution, there are thousands of atoms generating magnetic fields, all in random directions. Nuclear Magnetic Resonance Spectroscopy: Purpose: onnectivity, Map of - framework Process: In nuclear magnetic resonance spectroscopy, we are studying nuclei. onsider this circle to represent a nucleus

More information

Scattering Lecture. February 24, 2014

Scattering Lecture. February 24, 2014 Scattering Lecture February 24, 2014 Structure Determination by Scattering Waves of radiation scattered by different objects interfere to give rise to an observable pattern! The wavelength needs to close

More information

CHEM 3.2 (AS91388) 3 credits. Demonstrate understanding of spectroscopic data in chemistry

CHEM 3.2 (AS91388) 3 credits. Demonstrate understanding of spectroscopic data in chemistry CHEM 3.2 (AS91388) 3 credits Demonstrate understanding of spectroscopic data in chemistry Spectroscopic data is limited to mass, infrared (IR) and 13 C nuclear magnetic resonance (NMR) spectroscopy. Organic

More information

HWeb27 ( ; )

HWeb27 ( ; ) HWeb27 (9.1-9.2; 9.12-9.18) 28.1. Which of the following cannot be determined about a compound by mass spectrometry? [a]. boiling point [b]. molecular formula [c]. presence of heavy isotopes (e.g., 2 H,

More information

Structural characterization of complexes using NOESY experiments

Structural characterization of complexes using NOESY experiments Structural characterization of complexes using NOESY experiments Isotope labeling ( 3 C, 5 N) allows observation of individual components of a (binary) complex) H, 3 C, 5 N H, 3 C, 5 N 2 H/ H, 2 C, 4 N

More information

Spectroscopy in Organic Chemistry. Types of Spectroscopy in Organic

Spectroscopy in Organic Chemistry. Types of Spectroscopy in Organic Spectroscopy in Organic Chemistry Spectroscopy Spectrum dealing with light, or more specifically, radiation Scope to see Organic Spectroscopy therefore deals with examining how organic molecules interact

More information

Protein structure determination by solid-state NMR

Protein structure determination by solid-state NMR Protein structure determination by solid-state NMR Birgit Habenstein Supervised by Anja Böckmann Solid state NMR proteinaceous targets Structural studies and structure determination at atomic level Membrane

More information

Resonance assignments in proteins. Christina Redfield

Resonance assignments in proteins. Christina Redfield Resonance assignments in proteins Christina Redfield 1. Introduction The assignment of resonances in the complex NMR spectrum of a protein is the first step in any study of protein structure, function

More information

Calculate a rate given a species concentration change.

Calculate a rate given a species concentration change. Kinetics Define a rate for a given process. Change in concentration of a reagent with time. A rate is always positive, and is usually referred to with only magnitude (i.e. no sign) Reaction rates can be

More information

Determining Protein Structure BIBC 100

Determining Protein Structure BIBC 100 Determining Protein Structure BIBC 100 Determining Protein Structure X-Ray Diffraction Interactions of x-rays with electrons in molecules in a crystal NMR- Nuclear Magnetic Resonance Interactions of magnetic

More information

Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets

Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Supporting information Sensitive NMR Approach for Determining the Binding Mode of Tightly Binding Ligand Molecules to Protein Targets Wan-Na Chen, Christoph Nitsche, Kala Bharath Pilla, Bim Graham, Thomas

More information

Computational Methods for Mass Spectrometry Proteomics

Computational Methods for Mass Spectrometry Proteomics Computational Methods for Mass Spectrometry Proteomics Eidhammer, Ingvar ISBN-13: 9780470512975 Table of Contents Preface. Acknowledgements. 1 Protein, Proteome, and Proteomics. 1.1 Primary goals for studying

More information

Basic principles of multidimensional NMR in solution

Basic principles of multidimensional NMR in solution Basic principles of multidimensional NMR in solution 19.03.2008 The program 2/93 General aspects Basic principles Parameters in NMR spectroscopy Multidimensional NMR-spectroscopy Protein structures NMR-spectra

More information

Chapter 13 Spectroscopy

Chapter 13 Spectroscopy hapter 13 Spectroscopy Infrared spectroscopy Ultraviolet-Visible spectroscopy Nuclear magnetic resonance spectroscopy Mass Spectrometry 13.1 Principles of Molecular Spectroscopy: Electromagnetic Radiation

More information

Interpreting and evaluating biological NMR in the literature. Worksheet 1

Interpreting and evaluating biological NMR in the literature. Worksheet 1 Interpreting and evaluating biological NMR in the literature Worksheet 1 1D NMR spectra Application of RF pulses of specified lengths and frequencies can make certain nuclei detectable We can selectively

More information

Switching to OCR A from Pearson (Edexcel)

Switching to OCR A from Pearson (Edexcel) Switching to OCR A from Pearson (Edexcel) The content within the OCR Chemistry A specification covers the key concepts of chemistry and will be very familiar. We ve laid it out in a logical progression

More information

Chem 460 Laboratory Fall 2008 Experiment 3: Investigating Fumarase: ph Profile, Stereospecificity and Thermodynamics of Reaction

Chem 460 Laboratory Fall 2008 Experiment 3: Investigating Fumarase: ph Profile, Stereospecificity and Thermodynamics of Reaction 1 Chem 460 Laboratory Fall 2008 Experiment 3: Investigating Fumarase: ph Profile, Stereospecificity and Thermodynamics of Reaction Before Lab Week 1 -- ph Profile for Fumarase Read Box 11-1 (page 323)

More information

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease

NMR study of complexes between low molecular mass inhibitors and the West Nile virus NS2B-NS3 protease University of Wollongong Research Online Faculty of Science - Papers (Archive) Faculty of Science, Medicine and Health 2009 NMR study of complexes between low molecular mass inhibitors and the West Nile

More information

ORGANIC - EGE 5E CH NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY

ORGANIC - EGE 5E CH NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY !! www.clutchprep.com CONCEPT: PURPOSE OF ANALYTICAL TECHNIQUES Classical Methods (Wet Chemistry): Chemists needed to run dozens of chemical reactions to determine the type of molecules in a compound.

More information

Lecture 13 Organic Chemistry 1

Lecture 13 Organic Chemistry 1 EM 232 rganic hemistry I at hicago Lecture 13 rganic hemistry 1 Professor Duncan Wardrop February 23, 2010 1 EM 232 rganic hemistry I at hicago Spectroscopy & Spectrometry hapter 13 2 EM 232 rganic hemistry

More information

Hydrogen/Deuterium Exchange Mass Spectrometry: A Mini-Tutorial

Hydrogen/Deuterium Exchange Mass Spectrometry: A Mini-Tutorial Florida State University National High Magnetic Field Laboratory Tallahassee-Florida Hydrogen/euterium Exchange Mass Spectrometry: A Mini-Tutorial George Bou-Assaf 56 th ASMS Conference June 2 nd, 2008

More information

Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy

Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy Fluorescence and Nuclear Magnetic Resonance (NMR) Spectroscopy Murphy, B. (2017). Fluorescence and Nuclear Magnetic Resonance Spectroscopy: Lecture 3. Lecture presented at PHAR 423 Lecture in UIC College

More information

On the Approximability of the Maximum Interval Constrained Coloring Problem

On the Approximability of the Maximum Interval Constrained Coloring Problem S. Canzar 1 K. Elbassioni 2 A. Elmasry 3 R. Raman 4 On the Approximability of the Maximum Interval Constrained Coloring Problem 1 Centrum Wiskunde & Informatica, Amsterdam, The Netherlands 2 Max-Planck-Institut

More information

(b) How many hydrogen atoms are in the molecular formula of compound A? [Consider the 1 H NMR]

(b) How many hydrogen atoms are in the molecular formula of compound A? [Consider the 1 H NMR] CHEM 6371/4511 Name: The exam consists of interpretation of spectral data for compounds A-C. The analysis of each structure is worth 33.33 points. Compound A (a) How many carbon atoms are in the molecular

More information

Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent

Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent Figure S1. Interaction of PcTS with αsyn. (a) 1 H- 15 N HSQC NMR spectra of 100 µm αsyn in the absence (0:1, black) and increasing equivalent concentrations of PcTS (100 µm, blue; 500 µm, green; 1.5 mm,

More information

CHEM 393 Spectroscopy and Structure of Organic Compounds

CHEM 393 Spectroscopy and Structure of Organic Compounds CHEM 393 Spectroscopy and Structure of rganic Compounds According to Concordia s Centre for Teaching and Learning Services: F un I nteresting R ules S yllabus T est (pre-) C L A S S ommunity esson plan

More information

Lecture 14 Organic Chemistry 1

Lecture 14 Organic Chemistry 1 CHEM 232 Organic Chemistry I at Chicago Lecture 14 Organic Chemistry 1 Professor Duncan Wardrop February 25, 2010 1 CHEM 232 Organic Chemistry I at Chicago Mass Spectrometry Sections: 13.24-13.25 2 Spectroscopy

More information

(Refer Slide Time: 1:15)

(Refer Slide Time: 1:15) Principles and Applications of NMR spectroscopy Professor Hanudatta S. Atreya NMR Research Centre Indian Institute of Science Bangalore Module 1 Lecture No 01. Welcome every one. This is going to be a

More information

Technical Note. Introduction

Technical Note. Introduction Technical Note Characterization of Eleven 2,5-Dimethoxy-N-(2-methoxybenzyl)- phenethylamine (NBOMe) Derivatives and Differentiation from their 3- and 4- Methoxybenzyl Analogues - Part II Patrick A. Hays*,

More information

All measurement has a limit of precision and accuracy, and this must be taken into account when evaluating experimental results.

All measurement has a limit of precision and accuracy, and this must be taken into account when evaluating experimental results. Chapter 11: Measurement and data processing and analysis 11.1 Uncertainty and error in measurement and results All measurement has a limit of precision and accuracy, and this must be taken into account

More information

Unit 11 Instrumentation. Mass, Infrared and NMR Spectroscopy

Unit 11 Instrumentation. Mass, Infrared and NMR Spectroscopy Unit 11 Instrumentation Mass, Infrared and NMR Spectroscopy Spectroscopic identification of organic compounds Qualitative analysis: presence but not quantity (i.e. PEDs) Quantitative analysis: quantity

More information

E35 SPECTROSCOPIC TECHNIQUES IN ORGANIC CHEMISTRY

E35 SPECTROSCOPIC TECHNIQUES IN ORGANIC CHEMISTRY E35 SPECTRSCPIC TECNIQUES IN RGANIC CEMISTRY Introductory Comments. These notes are designed to introduce you to the basic spectroscopic techniques which are used for the determination of the structure

More information