NMR in biology: Structure, dynamics and energetics Gaya Amarasinghe, Ph.D. Department of Pathology and Immunology gamarasinghe@path.wustl.edu CSRB 7752 NMR? Nuclear Magnetic Resonance Spectroscopy Today, we will look at how NMR can provide insight in to biological macromolecules. This information often compliment those obtained from other structural methods. NMR Spectra contains a lot of useful information: from small molecule to macromolecule. • Few peaks • Sharper lines • Overall very easy to interpret http://www.cryst.bbk.ac.uk/PPS2/projects/schirra/html /1dnmr.htm • Many peaks • Broader lines • Overall NOT very easy to interpret http://www.nature.com/nature/journal/v418/n6894/fig_tab/ nature00860_F1.html • Structure determination by NMR • NMR relaxation– how to look at molecular motion (dynamics by NMR) • Ligand binding by NMR – Energetics Outline for Bio 5068 December 10 • Why study NMR (general discussion) 1.What is the NMR signal (some theory) 2.What information can you get from NMR (structure, dynamics, and energetic from chemical shifts, coupling (spin and dipolar), relaxation) 3.What are the differences between signal from NMR vs x-ray crystallography (we will come back to this after going through how to determine structures by NMR) • Practical aspects of NMR 1.instrumentation 2.Sample signal vs water signal 3.Sample preparation (very basic aspects & deal with specific labeling during the description of experiments) • Assignments and structure determination 1.2-D experiments 2.3/4-D experiments 3.Restraints and structure calculations • Assessing quality of structures 1.NMR structure quality assessment 2.Comparison with x-ray Diffractions For diffraction, the limit of resolution is ½ wavelength!! Electronic transitions Translational transitions Rotational transitions Nuclear transitions NMR works in the rf rangeafter absorption of energy by nuclei, dissipation of energy and the time it takes Reveals information about the conformation and structure. Protein Structures from an NMR Perspective Background – We are using NMR Information to “FOLD” the Protein. – We need to know how this NMR data relates to a protein structure. – We need to know the specific details of properly folded protein structures to verify the accuracy of our own structures. – We need to know how to determine what NMR experiments are required. – We need to know how to use the NMR data to calculate a protein structure. – We need to know how to use the protein structure to understand biological function Protein Structures from an NMR Perspective Analyzing NMR Data is a Non-Trivial Task! there is an abundance of data that needs to be interpreted X Not A Direct Path! Interpreting NMR Data Requires Making Informed “Guesses” to Move Toward the “Correct” Fold Distance from Correct Structure Initial rapid convergence to approximate correct fold Correct structure NMR Data Analysis Iterative “guesses” allow “correct” fold to emerge Current PDB statistics (as of 3/27/2012) Exp.Met Nucleic Protein/Nucleic Proteins Total hod Acids Acid Complexes X-RAY 65828 1346 3260 70436 NMR 8167 975 186 9335 ratio 8.06 1.38 17.53 Nuclei are positively charged many have a spin associated with them. Moving charge—produces a magnetic field that has a magnetic moment Spin angular moment Mass Charge I Even Even I=0 Even Odd I= integer Odd I=half integer How do we detect the NMR signal? •Practical aspects of NMR 1.instrumentation 2.Sample signal vs water signal 3.Sample preparation (very basic aspects & deal with specific labeling during the description of experiments) http://chem4823.usask.ca/nmr/magnet.html http://en.wikipedia.org/wiki/Nuclear_magnetic_resonance •Practical aspects of NMR 1.instrumentation 2.Sample signal vs water signal 3.Sample preparation (very basic aspects & deal with specific labeling during the description of experiments) http://www.chemistry.nmsu.edu/Instrumentat ion/NMSU_NMR300_J.html Sample preparation using recombinant methods Cell-free protein production and labeling protocol for NMR-based structural proteomics Vinarov et al., Nature Methods - 1, 149 - 153 (2004) Sample requirements and sensitivity Methyl groups are more sensitive than isolated Ha spins Source : www.chem.wisc.edu/~cic/nmr/Guides/Other/sensitivity-NMR.pdf Sample requirements and sensitivity mM not mM!! Cryoprobes are 3-4 times better S/N than standard probes (2x in high salt) Source : www.chem.wisc.edu/~cic/nmr/Guides/Other/sensitivity-NMR.pdf Why use NMR ? Some proteins do not crystallize (unstructured, multidomain) crystals do not diffract well can not solve the phase problem Functional differences in crystal vs in solution can get information about dynamics Protein Structures from an NMR Perspective Overview of Some Basic Structural Principals: a) Primary Structure: the amino acid sequence arranged from the amino (N) terminus to the carboxyl (C) terminus polypeptide chain b) Secondary Structure: regular arrangements of the backbone of the polypeptide chain without reference to the side chain types or conformation c) Tertiary Structure: the three-dimensional folding of the polypeptide chain to assemble the different secondary structure elements in a particular arrangement in space. d) Quaternary Structure: Complexes of 2 or more polypeptide chains held together by noncovalent forces but in precise ratios and with a precise three-dimensional configuration. Protein Structure Determination by NMR •Stage I—Sequence specific resonance assignment •State II – Conformational restraints •Stage III – Calculate and refine structure Resonance assignment strategies by NMR Illustrations of the Relationship Between MW, tc and T2 NMR Assignments 3D NMR Experiments • 2D 1H-15N HSQC experiment • correlates backbone amide 15N through one-bond coupling to amide 1H • in principal, each amino acid in the protein sequence will exhibit one peak in the 1H-15N HSQC spectra also contains side-chain NH2s (ASN,GLN) and NeH (Trp) position in HSQC depends on local structure and sequence no peaks for proline (no NH) Side-chain NH2 NMR Assignments 3D NMR Experiments • Consider a 3D experiment as a collection of 2D experiments z-dimension is the 15N chemical shift • 1H-15N HSQC spectra is modulated to include correlation through coupling to a another backbone atom Ci-1 O Ci O Ci Ni-1 Ci-1 Ci-1 Ni Ci H H H H • All the 3D triple resonance experiments are then related by the common 1H,15N chemical shifts of the HSQC spectra • The backbone assignments are then obtained by piecing together all the “jigsaw” puzzles pieces from the various NMR experiments to reassemble the backbone NMR Assignments 3D NMR Experiments • Amide Strip 3D cube 2D plane amide strip Strips can then be arranged in backbone sequential order to visual confirm assignments NMR Assignments 3D NMR Experiments • 3D HNCO Experiment common nomenclature letters indicate the coupled backbone atoms i i-1 (carbonyl carbon, CO or C’) correlates NH to C no peaks for proline (no NH) • Like the 2D 1H-15N HSQC spectra, each amino acid should display a single peak in the 3D HNCO experiment 1 15 identifies potential overlap in 2D H- N HSQC spectra, especially for larger MW proteins most sensitive 3D triple resonsnce experiment may observe side-chain correlations Ci-1 O Ni-1 1J NC’ Ci-1 Ci-1 Ni Ci O Ci Ci 1J NH H H H H NMR Assignments 3D NMR Experiments • 3D HN(CA)CO Experiment correlates NHi to COi i relays the transfer through C without chemical shift evolution uses stronger one-bond coupling contains only intra correlation provides a means to sequential connect NH and CO chemical shifts i i i i-1 (HNCO) match NH -CO (HN(CA)CO with NH -CO not sufficient to complete backbone assignments because of overlap and missing information every possible correlation is not observed need 2-3 connecting inter and intra correlations for unambiguous assignments no peaks for proline (no NH) breaks assignment chain but can identify residues i-1to prolines Ci-1 O Ci 1J NC Ni-1 Ci-1 Ci-1 1J CC’ Ni Ci H H 1J NH H H O Ci NMR Assignments 3D NMR Experiments • 3D HN(CA)CO Experiment Connects HNi-COi with HNi-COi-1 HNCO and HN(CA)CO pair for one residues NH Amide “Strips” from the 3D HNCO and HN(CA)CO experiments arranged in sequential order Journal of Biomolecular NMR, 9 (1997) 11–24 NMR Assignments 4D NMR Experiments • Consider a 4D NMR experiment as a collection of 3D NMR experiments still some ambiguities present when correlating multiple 3D triple-resonance experiments 4D NMR experiments make definitive sequential correlations increase in spectral resolution – Overlap is unlikely loss of digital resolution – need to collect less data points for the 3D experiment – If 3D experiment took 2.5 days, then each 4D time point would be a multiple of 2.5 days i.e. 32 complex points in A-dimension would require an 80 day experiment loss of sensitivity – an additional transfer step is required – relaxation takes place during each transfer Get less data that is less ambiguous? NMR Assignments Why use deuteration? • What are the advantages? • What are the disadvantages? Effects of Deuterium Labeling only 15N labeled 2D 15N-NH HSQC spectrum of the 30 kDa N-terminal domain of Enzyme I from the E. coli 15N, 2H labeled Current Opinion in Structural Biology 1999, 9:594–601 Protein Structure Determination by NMR •Stage I—Sequence specific resonance assignment •State II – Conformational restraints •Stage III – Calculate and refine structure NMR Structure Determination With The NMR Assignments and Molecular Modeling Tools in Hand: • All we need are the experimental constraints Distance constraints between atoms is the primary structure determination factor. Dihedral angles are also an important structural constraint What Structural Information is available from an NMR spectra? How is it Obtained? How is it Interpreted? NMR Structure Determination NOE NOE - a through space correlation (<5Å) - distance constraint 4.1Å 2.9Å Coupling Constant (J) - through bond correlation J NH CH - dihedral angle constraint Chemical Shift - very sensitive to local changes in environment - dihedral angle constraint Dipolar coupling constants (D) - bond vector orientation relative to magnetic field - alignment with bicelles or viruses CH D NH NMR Structure Determination Protein Secondary Structure and Carbon Chemical Shifts 1 IV 2 III 3 I II 4 NMR Structure Determination Protein Secondary Structure and Carbon Chemical Shifts • TALOS + NMR Structure Determination Protein Secondary Structure and 3JHN • Karplus relationship between f and 3JHN f =180o 3JHN = ~8-10 Hz -strand f = -60o 3JHN = ~3-4 Hz -helix Vuister & Bax (1993) J. Am.Chem. Soc. 115:7772 Protein Structure Determination by NMR •Stage I—Sequence specific resonance assignment •State II – Conformational restraints •Stage III – Calculate and refine structure Protein Structures from an NMR Perspective What Information Do We Know at the Start of Determining A Protein Structure By NMR? Effectively Everything We have Discussed to this Point! The primary amino acid sequence of the protein of interest. ► All the known properties and geometry associated with each amino acid and peptide bond within the protein. ► General NMR data and trends for the unstructured (random coiled) amino acids in the protein. The number and location of disulphide bonds. ► Not Necessary can be deduced from structure. 7 restraints/residue 10 restraints/residue 13 restraints/residue 16 restraints/residue Wüthrich et al. , J. Virol. February 15, 2009; 83:1823-1836 Analysis of the Quality of NMR Protein Structures With A Structure Calculated From Your NMR Data, How Do You Determine the Accuracy and Quality of the Structure? • Consistency with Known Protein Structural Parameters bond lengths, bond angles, dihedral angles, VDW interactions, etc all the structural details discussed at length in the beginning • Consistency with the Experimental DATA distance constraints, dihedral constraints, RDCs, chemical shifts, coupling constants all the data used to calculate the structure • Consistency Between Multiple Structures Calculated with the Same Experimental DATA Overlay of 30 NMR Structures Analysis of the Quality of NMR Protein Structures As We have seen before, the Quality of X-ray Structures can be monitored by an R-factor • No comparable function for NMR • Requires a more exhaustive analysis of NMR structures Analysis of the Quality of NMR Protein Structures Root-Mean Square Distance (RMSD) Analysis of Protein Structures • A very common approach to asses the quality of NMR structures and to determine the relative difference between structures is to calculate an rmsd an rmsd is a measure of the distance separation between equivalent atoms two identical structures will have an rmsd of 0Å the larger the rmsd the more dissimilar the structures 0.43 ± 0.06 Å for the backbone atoms 0.81 ± 0.09 Å for all atoms Analysis of the Quality of NMR Protein Structures Is the “Average” NMR Structure a Real Structure? • No-it is a distorted structure level of distortions depends on the similarity between the structures in the ensemble provides a means to measure the variability in atom positions between an ensemble of structures Expanded View of an “Average” Structure Some very long, stretched bonds Position of atoms are so scrambled the graphics program does not know which atoms to draw bonds between Some regions of the structure can appear relatively normal Analysis of the Quality of NMR Protein Structures As We Discussed Before, PROCHECK is a Very Valuable Tool For Accessing The Quality of a Protein Structure Correct f, y, c1, c2 distribution ► Comparison of main chain and side-chain parameters to standard values ► Protein Structures from an NMR Perspective Analyzing NMR Data is a Non-Trivial Task! there is an abundance of data that needs to be interpreted X Not A Direct Path! Interpreting NMR Data Requires Making Informed “Guesses” to Move Toward the “Correct” Fold Distance from Correct Structure Initial rapid convergence to approximate correct fold Correct structure NMR Data Analysis Iterative “guesses” allow “correct” fold to emerge Timescales of Protein Motion Energy landscape and dynamics high energy barriers = slow rate low energy barriers = fast rate H N Why do proteins move? • Broad, shallow energy potential – Thermal energy is sufficient for the protein to sample many different conformations • Change in conditions – Interaction with a small molecule or binding partner, change in temperature, ion concentration, etc. – Now a different conformation is lower in energy • Sequence encodes both protein structure and protein flexibility – Non-bonded interactions determine the lowest energy conformation(s) Function Stability Flexibility Sequence Function requires •Stability: the right chemical and spatial features in the right place to bind ligand, catalyze a chemical reaction, etc. •Flexibility: the ability to move in order to control access in and out of the active site and to provide energy for chemical reactions NMR Parameters for Protein Dynamics • • • • Number of signals per atom Line-widths Hydrogen Exchange (H-D) Hetero-nuclear {15N, 13C} Relaxation measurements – T1 (spin-lattice relaxation time) – T2 (spin-spin relaxation time) – Hetero-nuclear NOE NMR Analysis of Protein Dynamics Hydrogen-Deuterium Exchange • As we saw before, slow exchanging NHs allowed us to identify NHs involved in hydrogen-bonds. • Similarly, slow exchanging NHs are protected from the solvent and imply low dynamic regions. • Fast exchanging NHs are accesible to the solvent and imply dynamic residues, especially if not solvent exposed. Protein sample is exchanged into D2O and the disappearance of NHs peaks in a 2D 1H-15NH spectra is monitored. Protein Science (1995), 4:983-993. NMR Analysis of Protein Dynamics Hydrogen-Deuterium Exchange • As expected, majority of NHs that exhibit slow exchange rates are located in secondary structures • fast exchanging NHs are located in loops, N- and C-terminal regions NMR Relaxation After an RF pulse system needs to relax back to equilibrium condition Related to molecular dynamics of system may take seconds to minutes to fully recovery usually occurs exponentially: (n ne )t = (n ne )0 exp( t / T ) – – (n-ne)t displacement from equilibrium value ne at time t (n-ne)0 at time zero Relaxation can be characterized by a time T – relaxation rate (R): 1/T No spontaneous reemission of photons to relax down to ground state Two types of NMR relaxation processes spin-lattice or longitudinal relaxation (T1) spin-spin or transverse relaxation (T2) z Mo B1 z B1 off… x Mxy (or off-resonance) y z y w1 Mo T1 & T2 relaxation y x NMR Relaxation Spin-lattices or longitudinal relaxation Relaxation process occurs along z-axis transfer of energy to the lattice or solvent material coupling of nuclei magnetic field with magnetic fields created by the ensemble of vibrational and rotational motion of the lattice or solvent. results in a minimal temperature increase in sample Relaxation time (T1) exponential decay Mz = M0(1-exp(-t/T1)) NMR Relaxation Spin-Spin or Transverse relaxation Relaxation process in the x,y plane Related to peak line-width – T2 may be equal to T1, or differ by orders of magnitude – Inhomogeneity of magnet also contributes to peak width T2 can not be longer than T1 No energy change T2 relaxation (derived from Heisenberg uncertainty principal) NMR Relaxation Mechanism for Spin-lattices and Spin-Spin relaxation • Illustration of the Relationship Between MW, tc and T2 Conformational Exchange Increases the Rate of Transverse Relaxation (R2) in NMR Spectra R2 = R20 + Rex Rex depends on: Kinetics: kex = kA + kB Thermodynamics: pA*pB Structure: Dw NMR Analysis of Protein Dynamics k = p Dno2 /2(he - ho) k = p Dno / 21/2 k = p (Dno2 - Dne2)1/2/21/2 k = p (he-ho) k – exchange rate n – peak frequency h – peak-width at half-height e – with exchange o – no exchange In the Absence of Chemical Exchange Magnetization Refocuses Following a 180° Pulse PreparationPreparationRelaxation Frequency Labeling Acquisition Relaxation Due to Chemical Exchange Leads to Loss of Transverse Magnetization Preparation Relaxation Frequency Labeling No Chemical Exchange With Chemical Exchange Acquisition Increasing the Number of CPMG Pulses Can Recover Magnetization Due to Rex Relaxation · · · Frequency Labeling Acquisition R2 (1/s) Preparation Rex R20 pulse rate (1/s) For 2-state exchange in the ms-µs regime, quantitative analysis can in principle yield: pA, pB, kA, kB, Dw Summary --- NMR relaxation/dynamics • High sensitivity and site specific information • may need isotopic labeling •May require assignment of resonances • Can help narrow construct space and identify interfaces •regions that interact with solvent or binding partners NMR Analysis of Protein-Ligand Interactions NMR Monitors the Different Physical Properties That Exist Between a Protein and a Ligand NMR Analysis of Protein-Ligand Interactions Ligand Line-Width (T2) Changes Upon Protein Binding • As we have seen before, line-width is directly related to apparent MW a small-molecule (~100-1,000Da) is orders of magnitude lighter than a typical protein (10s of KDa) a small molecule has sharp NMR line-widths (few Hz at most)) protein has broad line-widths (10s of Hz) if a small molecule binds a protein, its line-width will resemble the larger MW protein tc MW/2400 (ns) + Small molecule: Sharp NMR lines Broad NMR lines Chemical exchange NMR timescales • Slow isomerization of dimethyl amino group at low temperature produces distinct signals for each methyl • At increasing temperatures (faster exchange rates) peaks broaden and eventually coalesce into one average signal • For binding reactions, slow exchange (higher affinity) produces distinct signals for free and bound states at intermediate titration points - follow binding reaction by watching bound/free peak intensities grow/diminish • Fast exchange - only one set of peaks throughout titration, shifting in proportion to changing ratio of free:bound Summary --- NMR ligand binding • High sensitivity and site specific information • may need isotopic labeling •May require assignment of resonances • Affinity measurements are only valid for low affinity interactions • Complex structures can be determined for high affinity interactions Final thoughts? Some Other Recommended Resources “NMR of Proteins and Nucleic Acids” Kurt Wuthrich “Protein NMR Spectroscopy: Principals and Practice” John Cavanagh, Arthur Palmer, Nicholas J. Skelton, Wayne Fairbrother “Principles of Protein Structure” G. E. Schulz & R. H. Schirmer “Introduction to Protein Structure” C. Branden & J. Tooze “Enzymes: A Practical Introduction to Structure, Mechanism, and Data Analysis” R. Copeland “Biophysical Chemistry” Parts I to III, C. Cantor & P. Schimmel “Principles of Nuclei Acid Structure” W. Saenger Some Important Web Sites: RCSB Protein Data Bank (PDB) http://www.rcsb.org/pdb/ Database of NMR & X-ray Structures BMRB (BioMagResBank) http://www.bmrb.wisc.edu/ Database of NMR resonance assignments CATH Protein Structure Classification Classification of All Proteins in PDB http://www.biochem.ucl.ac.uk/bsm/cath/ SCOP: Structural Classification of Proteins Classification of All Structures into http://scop.berkeley.edu Families, Super Families etc. DALI http://www.ebi.ac.uk/dali/ Compares 3D-Stuctures of Proteins to Determine Structural Similarities of New Structures NMR Information Server http://www.spincore.com/nmrinfo/ NMR Groups, News, Links, Conferences, Jobs NMR Knowledge Base http://www.spectroscopynow.com/ A lot of useful NMR links Many slides have been either taken directly or adapted from the following sources: http://www.bionmr.com/forum/educational-web-pages-16/lectures-nmr-spectroscopyprotein-structures-university-nebraska-lincoln-324/ David Cistola (Wash U) Kevin Gardner/Carlos Amzcua (UTSW) Or as cited Some examples of how NMR can provide information about biological systems Non-self dsRNA recognition is inhibited by filoviral VP35 at multiple steps in the IFN production pathway zVP35/mVP35 IFITs (1,2,3) Leung et al, 2011 Virulence VP35 IID structure revealed two functionally important conserved basic patches viral replication “first” basic patch IFN inhibition “central” basic patch All VP35 binders contain a common pyrrollidinone scaffold NMR-based studies reveal quantitative structure/activity relationships (QSAR) NMR provides a medium throughput quantitation of ligand binding A subset of residues important for VP35-NP binding are also important for inhibitor binding Crystal structure(s) of Zaire ebolavirus IID-GA228 complex reveals key protein-small molecule contacts ~30 different small molecule-VP35 IID structures provides a comprehensive SAR dataset Currently, the efficacy and PD/PK characteristics are being tested. Autoinhibited Multi-Domain Proteins are Critical in Many Signal Transduction Pathways • Numerous multi-domain proteins transmit signals from the T-cell receptor Rosen lab Vav proto-oncoprotein is a key GEF that regulates Rho family GTPases • A member of the Dbl family of guanine nucleotide exchange factors (GEF) for the Rho family of GTP binding proteins. • Important in hematopoiesis, playing a role in T-cell and B-cell development and activation. • DH domain is inhibited by contacts with the Acidic (Ac) region and is relieved by phosphorylation of the Ac region tyrosines A Helix From the Ac Domain Binds in the DH Active Site: Autoinhibition by Occlusion Aghazadeh, et al. Cell, 102: 625-633. • Y3 is buried in the interface Phosphorylation Disrupts Autoinhibitory Interactions Aghazadeh, et al. Cell, 102: 625-633. • Amide resonances from N-terminal (Ac region) helix collapse to the center of the 1H/15N HSQC spectra and become extremely intense • 13C and 13C assignments indicate that the N-terminus is random coil How is Y3 Accessed by Kinases? A general problem in autoinhibition/allostery: activators must contact buried sites ? Chemical Shift Can Report on Population Distribution • Linearity of chemical closed shifts across multiple perturbations indicates a two-state equilibrium 50:50 mixture open wobs = powo + (1-po)wc Mutants Sample a Range of Population Distributions Open Closed • Linearity strongly suggests an equilibrium between Y3bound and Y3-unbound states wobs = powo + (1-po)wc Conformational equilibrium controls Vav activation by Src family kinases Vav WASP/Cdc42 Science. 1998 Jan 23;279(5350):509-14. Nature. 2000 Mar 9;404(6774):151-8. Nature. 1999 May 27;399(6734):379-83. Rosen lab