3J Scalar Couplings 3 J HN-H  The 3 J coupling constants are related to the dihedral angles by the Karplus equation, which is an empirical relationship.

Slides:



Advertisements
Similar presentations
Modern Approaches to Protein structure Determination (6 lectures)
Advertisements

Relaxation Time Phenomenon & Application
Lecture 17. Light Scattering/Viscometry. What is light scattering? In the lab…
Introduction to protein x-ray crystallography. Electromagnetic waves E- electromagnetic field strength A- amplitude  - angular velocity - frequency.
Experimental Techniques in Protein Structure Determination Homayoun Valafar Department of Computer Science and Engineering, USC.
(random-orientation)
Computing Protein Structures from Electron Density Maps: The Missing Loop Problem I. Lotan, H. van den Bedem, A. Beacon and J.C. Latombe.
Lecture 3 – 4. October 2010 Molecular force field 1.
Incorporating additional types of information in structure calculation: recent advances chemical shift potentials residual dipolar couplings.
Structure Determination by NMR CHY 431 Biological Chemistry Karl D. Bishop, Ph.D. Lecture 1 - Introduction to NMR Lecture 2 - 2D NMR, resonance assignments.
Biomolecular Nuclear Magnetic Resonance Spectroscopy BIOCHEMISTRY BEYOND STRUCTURE Protein dynamics from NMR Analytical Biochemistry Comparative Analysis.
Biomolecular Nuclear Magnetic Resonance Spectroscopy BIOCHEMISTRY BEYOND STRUCTURE Protein dynamics from NMR Analytical biochemistry Comparative analysis.
NMR spectra of some simple molecules Effect of spinning: averaging field inhomogeneity (nmr1.pdf pg 2)
Lecture 3 The Debye theory. Gases and polar molecules in non-polar solvent. The reaction field of a non-polarizable point dipole The internal and the direction.
Solving NMR structures I --deriving distance restraints from crosspeak intensities in NOESY spectra --deriving dihedral angle restraints from J couplings;
Data Analysis Issues in Time-Resolved Fluorescence Anisotropy Bill Laws Department of Chemistry University of Montana Support from NSF EPSCoR, NIH, and.
A Kinematic View of Loop Closure EVANGELOS A. COUTSIAS, CHAOK SEOK, MATTHEW P. JACOBSON, KEN A. DILL Presented by Keren Lasker.
Modeling of protein turns and derivation of NMR parameters related to turn structure Megan Chawner BRITE REU Program Advisor: Dr. Dimitrios Morikis Department.
Scalar and Vector Fields
Joel R. Tolman Department of Chemistry Johns Hopkins University Residual Dipolar Couplings II EMBO Course 2009 Rosario, Argentina.
How NMR is Used for the Study of Bio-macromolecules Analytical biochemistry Comparative analysis Interactions between biomolecules Structure determination.
Molecular Modeling Part I Molecular Mechanics and Conformational Analysis ORG I Lab William Kelly.
Chapter 12 Protein Structure Basics. 20 naturally occurring amino acids Free amino group (-NH2) Free carboxyl group (-COOH) Both groups linked to a central.
Angular Dependence of 3-bond J-couplings
4. The Nuclear Magnetic Resonance Interactions 4a. The Chemical Shift interaction The most important interaction for the utilization of NMR in chemistry.
Residual Dipolar Couplings ;RDC Cheng-Kun Tsai Cheng-Kun Tsai
Introduction to biological NMR Dominique Marion Institut de Biologie Structurale Grenoble France.
Two models for the description of light The corpuscular theory of light stating that light can be regarded as a stream of particles of discrete energy.
NMR Analysis of Protein Dynamics Despite the Typical Graphical Display of Protein Structures, Proteins are Highly Flexible and Undergo Multiple Modes Of.
Comparing Data from MD simulations and X-ray Crystallography What can we compare? 3D shapes (Scalar coupling constants, a.k.a. J-values, nuclear Overhauser.
Biomolecular Nuclear Magnetic Resonance Spectroscopy BASIC CONCEPTS OF NMR How does NMR work? Resonance assignment Structure determination 01/24/05 NMR.
Absorption and Emission of Radiation:
Protein Dynamics from NMR 03/19/02 Protein and Peptide Drug Analysis, pages Amide proton exchange Heteronuclear relaxation Application to determine.
Biomolecular Nuclear Magnetic Resonance Spectroscopy FROM ASSIGNMENT TO STRUCTURE Sequential resonance assignment strategies NMR data for structure determination.
1 M.Sc. Project of Hanif Bayat Movahed The Phase Transitions of Semiflexible Hard Sphere Chain Liquids Supervisor: Prof. Don Sullivan.
Investigations of Membrane Polypeptides by Solid-state NMR Spectroscopy: Structure, Dynamics, Aggregation and Topology of Supramolecular Complexes Burkhard.
The number of protons yielding correlations in a 2D NOESY spectrum quickly overwhelms the space available on A 2D map. 15N labeling can help simplify the.
03/27/09 NIH Roadmap Structure Determination of Membrane Proteins from Orientational Constraints Homayoun Valafar Roadmap Initiative Meeting 3/26/09-3/27/09.
Förster Resonance Energy Transfer (FRET)
Residual dipolar couplings in NMR structure determination
3D Triple-Resonance Methods for Sequential Resonance Assignment of Proteins Strategy: Correlate Chemical Shifts of Sequentially Related Amides to the Same.
Dipole radiation during collisions LL2 Section 68.
PE: Hydration, enthalpy and entropy. Intermediate structures Between Phases.
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.
These 2D methods work for proteins up to about 100 amino acids, and even here, anything from amino acids is difficult. We need to reduce the complexity.
Stony Brook Integrative Structural Biology Organization
Biophysical Tools '04 - NMR part II
Douglas Kojetin, Ph.D. UC College of Medicine
Dielectrics 11/10/08.
Volume 12, Issue 12, Pages (December 2004)
1. Pure Protein (0.3 mL, mM; ~ 10 mg)
Structure and Dynamics of the Membrane-Bound Form of Pf1 Coat Protein: Implications of Structural Rearrangement for Virus Assembly  Sang Ho Park, Francesca.
SH3-SH2 Domain Orientation in Src Kinases
Department of Chemistry North Eastern Hill University
Richard C. Page, Sanguk Kim, Timothy A. Cross  Structure 
Volume 15, Issue 9, Pages (September 2007)
Volume 83, Issue 2, Pages (August 2002)
Volume 83, Issue 2, Pages (August 2002)
A Conformational Switch in the CRIB-PDZ Module of Par-6
Richard C. Page, Sanguk Kim, Timothy A. Cross  Structure 
Volume 96, Issue 6, Pages (March 2009)
CHY 431 Biological Chemistry
Volume 112, Issue 12, Pages (June 2017)
Proteins Have Too Many Signals!
Solution Structure of the Proapoptotic Molecule BID
Volume 23, Issue 6, Pages (June 2015)
Mechanism of Interaction between the General Anesthetic Halothane and a Model Ion Channel Protein, III: Molecular Dynamics Simulation Incorporating a.
Volume 98, Issue 4, Pages (February 2010)
Emmanuel O. Awosanya, Alexander A. Nevzorov  Biophysical Journal 
Presentation transcript:

3J Scalar Couplings 3 J HN-H  The 3 J coupling constants are related to the dihedral angles by the Karplus equation, which is an empirical relationship obtained from molecules for which the crystal structure is known. The equation is a sum of cosines, and depending on the type of topology (H-N-C-H or H-C-C-H) we have different parameters: 3 J N  = 9.4 cos 2 (  - 60 ) cos(  - 60 ) J  = 9.5 cos 2 (  - 60 ) cos(  - 60 ) Sometimes 3 J has no unique solution and extra information is required! CS, NOE, Ramachandran plot!

Measurement of Couplings Problem: large linewidth, no splitting quantitative J experiments J is calculated from an intensity ratio

IPAP-HSQC Measure 1 J HN-N by combining an InPhase and an AntiPhase HSQC

J-Correlation through H-Bonds ubq.pdb H-N-C’ and H-N … O=C’ Correlations e- density in the H-bond

B 0 Dependence of Splittings Indicates Dipolar Contributions Incomplete averaging of the dipolar interaction due to partial alignment in the magnetic field  IS =h*  I  S /r IS 3 (3cos 2  IS -1) Angular dependance allows the measurement of angles and relative orientations, which has not been possible in NMR Contains information about angles !

Field induced Alignment Dipolar Contribution to J Splitings Proportional to B 0 2, but effects are very small Few Hz in molecules with a large magnetic anisotropy e.g. 2gat.pdb ‘Artificial’ Alignment required D IS is measured as the different splitting between different B 0 fields

Induced Alignment Phospholipid ‘Bicelles’ colloidal Phage particles ---- Surfaces may be additionally charged to modulate the alignment sample stability can be a BIG problem

NMR in LC Phases

NMR in Liquid Crystals

Dipolar couplings along a Protein Backbone Measured as difference in splitting between aligned (left) and isotropic phase (right)  IS =J IS +D IS

Dipolar Coupling The magnitude of the residual dipolar coupling depends on the alignment tensor: 5 parameters Da/Dr: magnitude and rhombicity + 3 rotation angles: orientation relative to the.pdb frame Knowing the alignment tensor (e.g. by least squares fitting) DC can be simulated and compared to experimental data (in the principal axis frame)

Motion along a Cone dipolar couplings can be used as restraints in NMR structure determination The measurement of a residual dipolar coupling limits the the orientation of a bond vector (relative to the alignment tensor) to a narrow cone on a unit sphere It restricts the orientaion relative to a ‘global’ alignment frame not relative to other vectors

Two Tensors! almost unique solution (intersection of cones)

Dipolar Homology Arbitrary fragments from the.pdb are fitted to the collected dipolar couplings The dipolar agreement is used for the scoring The best fragments are kept

Dipolar Homology Mining use measured DC to search for matching overlapping peptide fragments

Molecular Fragment Replacement Fragments must share one common alignment frame So the relative orientation can be inferred Ambiguities: 0, 180x, 180y, 180z can be resolved by coordinate overlap Use ‘Long Range Information in the Assembly Process

Assemble a Protein Structure

Protein Structure by MFR