Practical 10: Protein dynamics and visualization
Contents
1. The NMP domain consisting of helices H2 H4 residues 30 59 and the LID domain H6 and two small beta sheets B1 B2 and C1 C2 C3 resids 122 159 are very mobile On closing the both fold towards CORE on hinges When RMS fitted on CORE the overall RMSD is 8 0 AdK Ligand The AP5 ligand mimics the transition state of the phospho transfer reaction Phosphates are negatively charged hence only basic positively charged blue residues are in contact 2 2 Exercises 7 Practical 10 Protein dynamics and visualization Documentation Release 1 0 Topology of AdK C3 Figure 2 2 Topology diagram of AdK 8 4 zing protein structure and topology V j j d XL wp a SZ Practical 10 Protein dynamics and visualization Documentation Release 1 0 2 2 Exercises 9 Practical 10 Protein dynamics and visualization Documentation Release 1 0 10 Chapter 2 Analyzing protein structure and topology CHAPTER THREE PUBLICATION QUALITY IMAGES To make an image with AO ambient occlusion lighting and depth cueing Settings Display gt Rendermode gt GLSL Display Display Settings Shadows On Amb Occl On Cue Mode Linear Cue start 1 75 Cueend 3 0 white bg Graphics Colors Display White rendering File gt Render snapshot glossy material looks nice tachyon internal ray tracer takes a while due to AO change materials to spec2. natural aa L form note look down H Ca and read CORN L otherwise D peptide bond repeating unit residue same backbone differing sidechain R sequence primary structure hydrogen bonds donor H acceptor secondary structure alpha helix n n 4 H bonds of main chain 3 6 res per turn peptide units phi psi angles flexible omega peptide bond fixed cis trans must be right handed otherwise clashes only very short helices are left handed beta sheet extended parallel anti parallel coiled coil 3 10 helix n n 3 10 atoms between donor and acceptor 3 res per turn pi helix n n 5 tertiary structure helices sheets hairpins loops coiled coil quaternary structure Practical 10 Protein dynamics and visualization Documentation Release 1 0 4 Chapter 1 Basics of protein structure CHAPTER TWO ANALYZING PROTEIN STRUCTURE AND TOPOLOGY Use VMD to learn more about a protein The example we use is adenylate kinase AdK For background on using VMD look at Hsin2008 and the VMD tutorial 2 1 Topology and 2ndary structure get adk open pdb from http becksteinlab physics asu edu pages courses 2013 SimBioNano 09 settings in VMD Display Orthographic Display gt Rendermode GLSL Graphics gt Color Display Background White select protein new cartoon representation color by secondary structure 2 2 Exercises
3. Practical 10 Protein dynamics and visualization Documentation Release 1 0 14 Chapter 4 Analyzing protein dynamics CHAPTER FIVE MAKING MOVIES IN VMD 5 1 Install the ffmpeg encoder The iMAcs are not well equipped for movie making so we need to install the ffmpeg encoder from http becksteinlab physics asu edu pages courses 2013 SimBioNano 10 ffmpeg cd bin curl O http becksteinlab physics asu edu pages courses 2013 SimBioNano 10 ffmpeg ffmpeg chmod a x ffmpeg Then make sure that ffmpeg is found on your PATH echo export PATH SHOME bin SPATH gt gt profile You might have to log out and log in for this to have full effect later on 5 2 AdK transition movie We use the standard VMD plugin MovieMaker 1 Load the AdK transition trajectory from Analyzing protein dynamics 2 Use a nice representation e g color the CORE LID and NMP domains You can also find a number of salt bridges pairs of basic positively charged and acidic negatively charge residues that zip up AdK see the AdK zipping movie from Beckstein et al 3 Open Extension Visualization gt Movie Maker 4 Settings e Renderer Snapshot for Hollywood style movies use one of the ray tracers such as tachyon AO Movie Settings Trajectory Set Format to MPEG 1 ffmpeg MPEG 2 is better but the iMacs can t display it e Set your working directory to e g USERNAME p10 movies so that you can easily f
4. 2 2 1 Identify secondary structure and topology Sketch a topology diagram on paper use open structure for analysis number helices H1 H8 ignore short 4 res count all helices as helix alpha pi 3 10 sheets A B C number strands SA1 SA5 SB1 3 SC1 2 start with central b sheet locate N terminus resid 1 and name CA color blue VDW and C terminus Note Youcandoranges resid 1 to 5ormultipleranges resid 1 to 5 20 to 50 You can use boolean operators and or not See selections in the user manual for details draw connections between secondary elements in your topology diagram and label secondary structure elements Practical 10 Protein dynamics and visualization Documentation Release 1 0 Topology of AdK a 4X H6 H8 Figure 2 1 Topology diagram of AdK 2 2 2 Identify domains tertiary structure compare to closed conformation load adk closed pdb select protein new cartoon color differently from the open structure superimpose Extensions Analysis RMSD tool protein N RMSD 2 e What is the RMSD after superposition Investigate how the conformation of the molecule changes Which regions domains move Identify two moving domains called NMP and LID and one constant region CORE give residue ranges tip use Extensions gt Analysis gt Sequence Viewer color regions differently and also mark them in your topol
5. Practical 10 Protein dynamics and visualization Documentation Release 1 0 Oliver Beckstein March 07 2013 1 Basics of protein structure 2 Analyzing protein structure and topology 2 1 Topology and2ndary structure 2 2 Exelcises 22 2 x Ro eee m x 3 Publication quality images 4 Analyzing protein dynamics 4 Visualization 2 254245 ose xem dens 42 RMSD changes 2 2 88 aoe a RR 4 3 Measuring distances sen 5 Making movies in VMD 5 1 Install the ffmpeg encoder 5 2 AdK transition movie 5 3 Advanced movie making 222000 6 Learning Objectives 7 References 8 Indices and tables Bibliography Index CONTENTS 11 13 Bf nip as sha ae Br eL dune eri RE 13 Br seen 4 eR Tene 13 TIT I Meere 13 15 e are re I de teen Se 15 1 15 bi Sy at dece Gh got dos ie dtes dre de Bice ms 16 17 19 21 23 25 Practical 10 Protein dynamics and visualization Documentation Release 1 0 For background on using VMD look at Hsin2008 and the VMD tutorial Basics of protein structure are illustrated in BrandenTooze Contents CONTENTS 1 Practical 10 Protein dynamics and visualization Documentation Release 1 0 2 CONTENTS CHAPTER ONE BASICS OF PROTEIN STRUCTURE See also illustrations in slides and BrandenTooze Introduction to protein structure polypeptides amino acids chemical structure of the 20 aa
6. c analysis use of RMSFitting tools 17 Practical 10 Protein dynamics and visualization Documentation Release 1 0 18 Chapter 6 Learning Objectives CHAPTER SEVEN REFERENCES Practical 10 Protein dynamics and visualization Documentation Release 1 0 20 Chapter 7 References CHAPTER EIGHT INDICES AND TABLES 21 Practical 10 Protein dynamics and visualization Documentation Release 1 0 22 Chapter 8 Indices and tables BIBLIOGRAPHY BrandenTooze C Branden and J Tooze Introduction to Protein Structure 2nd ed 1999 Garland Publishing New York Hsin2008 J Hsin A Arkhipov Y Yin J E Stone and K Schulten Using VMD An Introduc tory Tutorial volume 24 chapter 5 7 pages 5 7 1 5 7 48 John Wiley amp Sons Inc 2008 URL http dx doi org 10 1002 0471250953 bi0507s24 Beckstein2009 O Beckstein EJ Denning JR Perilla and TB Woolf Zipping and Unzipping of Adenylate Ki nase Atomistic Insights into the Ensemble of Open Closed Transitions J Mol Biol 394 2009 160 176 http dx doi org 10 1016 j jmb 2009 09 009 23 Practical 10 Protein dynamics and visualization Documentation Release 1 0 24 Bibliography E environment variable PATH 15 P PATH 15 INDEX 25
7. ial AO materials e g AOChalky 11 Practical 10 Protein dynamics and visualization Documentation Release 1 0 Figure 3 1 Example AdK was rendered with Tachyon internal with VDW representation colors silver yellow and blue no depth cueing material AOChalky and using Ambient Occlusion AO and Shadows see Display Displaysettings 12 Chapter 3 Publication quality images CHAPTER FOUR ANALYZING PROTEIN DYNAMICS Analyze a trajectory of the closed to open transition of AdK Beckstein2009 4 1 Visualization e load adk psf with adk dims dcd use load all at once this is faster in general color domains and show as new cartoon resid 30 to 59 blue resid 122 to 159 yellow not resid 30 to 59 122 to 159 or resid 1 to 29 60 to 121 160 to 214 gray play loop rock 4 2 RMSD change RMSD change over the trajectory Extensions Analysis RMSD Trajectory Tool s the result consistent with the result of your RMSD analysis of the static structures 4 3 Measuring distances Measure distances interactively 2 or Mouse Label gt Bonds click tip of LID and tip of NMP play the trajectory label changes dynamically Graphics Labels Bonds select Graph preview Graph try different distances between residues use the CA and plot together which change which don t What would be good distances to report on conformational changes e g for FRET 13
8. ind the finished movie Name your movie e g adk transition 5 Make Movie should step through your trajectory write out frames and finally run ffmpeg 6 In the shell go to your movie directory and play it 15 Practical 10 Protein dynamics and visualization Documentation Release 1 0 open adk transition mpg 5 3 Advanced movie making In order to rotate and zoom a movie during a trajectory we can use the VMD ViewChangeRender plugin together with MovieMaker Open ViewChangeRender Extensions gt Visualization gt ViewChangeRender Generate viewpoints of your movie 1 Adjust position in trajectory rotate zoom 2 Save Viewpoint Repeat for as many viewpoints as you want to include Add all viewpoints to movie The final movie will smoothly interpolate between these points You can check with Preview Movie Note that this plugin has a few bugs so you might have to quit and restart when it stops working Once you are ready to render the movie 1 In ViewChangeRender Enable 2 In MovieMaker a Movie Settings User defined procedure b Adjust other settings as needed c Make movie 16 Chapter 5 Making movies in VMD CHAPTER SIX LEARNING OBJECTIVES basic understanding of protein structure familiarize with a molecular graphics program VMD loading of static structures and dynamics trajectories viewing a molecule mouse view modes representations selections making images basi
9. ogy diagram align on CORE domain only What is the final RMSD when aligned on CORE only i e how similar are the CORE regions in the two structures What is the overall protein RMSD assuming that the two structures are superimposed on CORE 6 Chapter 2 Analyzing protein structure and topology Practical 10 Protein dynamics and visualization Documentation Release 1 0 2 2 3 Ligands e Download 1 AKE from the PDB or use lake pdb from the course directory show protein chain A show the co crystallized ligand Ap5 resname AP5 resname AP5 licorice color name show charged residues within 5 of the ligand same residue as charged and within 5 of resname AP5 use representation icorice color name for the residues make ligand VDW Which side chains make contact with the ligand What have they got in common Tip try out color restype water show crystal water oxygens as VDW or licorice small spheres 2 2 4 Summary AdK secondary and tertiary structure AdK is a dynamic enzyme which can undergo a large conformational change between an open and a closed confor mation The backbone RMSD between the two conformations is about 7 16 A AdK contains a central beta sheet with strands A1 to A5 between four helices H1 H5 H7 H8 making up the CORE domain residues 1 29 60 121 160 214 This CORE domain does not change much between the open and closed conformation RMSD 1 97 of CORE
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