Practical Macromolecular 3D Structure Visualization & Structural Bioinformatics
A One-Day Workshop --
Osaka University, Japan
Friday, May 8, 2015, 9:00 - 17:00, Biosystems Building, Room E203.
Bringing A Laptop Computer Is Encouraged
Host and Co-Instructor:
Thanks to Tohru Minamino and Kana Moriya Nishimura.
Yurika Yamada, Péter Horváth, Tomofumi Sakai.
, Ph.D.: Lead Instructor.
Principal author of FirstGlance in Jmol; co-developer of Proteopedia and the ConSurf Server.
Professor Emeritus, University of Massachusetts, Amherst --
This document is on-line:
Objectives: Participants will use highly user-friendly
software for visual investigation of 3D molecular structures of
proteins, nucleic acids, and their interactions with each other
and with ligands, substrates, and drugs; and of protein evolutionary
conservation. Hands-on experience will be largely with molecules
of each participant's choosing. Participants will learn how to
create publication-quality molecular images and rotating molecules
in Powerpoint slides.
All software in this course is free, and works on Windows, Mac OS X, or linux.
Level & Pace: This workshop is designed for faculty, postdocs,
research staff and graduate students
familiar with basic biochemistry, but with no
previous molecular visualization software experience.
It progresses rapidly to powerful tools that will be of interest
to specialists in protein structure and bioinformatics.
Experienced participants are encouraged to work at their own speed,
ahead of the group -- there is plenty of power to discover within
Explanations of structural biology terms and concepts, e.g.
asymmetric unit, Protein Data Bank, hydrogen bonds, temperature value,
etc. all at
About Macromolecular Structure.
Japanese, Chinese, Arabic, Turkish, Russian, etc.
Each person please get started:
If you brought your own laptop, you are welcome use it. (iPads will be too slow.)
Use the Chrome browser. If you do not have it, take a few minutes to install it
(Chrome will be faster/smoother than Safari, and Firefox is even slower for this software.
Internet Explorer and Opera are unusably slow with this software.)
In the Chrome browser, go to our syllabus: Workshops.MolviZ.Org.
Now you can see this document in your browser.
In the Atlas, choose any molecule deemed Straightforward and click on the link
to FirstGlance. After a minute or so to load, you should see a rotating molecule.
Have a look around at the information, views and tools in FirstGlance.
If you have any difficulty or the molecule does not appear, or does not rotate, ask for help!
OPTIONAL: Installing and Enabling Java
You can see molecules without Java, using
in the primary tool
of this course:
For some older sites that display molecules in Jmol,
or for especially large molecules,
you may need to
install and enable Java.
Java will also make FirstGlance run faster and smoother.
In this course, there are resources that use all of the 3 forms of Jmol that work in web browsers:
four forms of Jmol.
- JSmol (no Java)
- Jmol_S (signed Java applet)
- Jmol (unsigned Java applet,
instructions for installing/updating and enabling Java.
- TA's and Instructors will help you!
- Can you see this
Gal4:DNA complex with Java
- If you got Java to work, use the Preferences tab in
FirstGlance to make Java the default. Then
this link to Gal4:DNA
should use Java
- Some sites use an older, unsigned
Java applet. An example
is this explanation of
Protein Secondary Structure. Can you see the molecule?
Make sure to
Enable Unsigned Java Applets
for this website. Later in the course, you may want to enable other
Workshop Overview (Powerpoint Slides)
Proteopedia.Org Part I
Protein Data Bank & PDB Codes
The Protein Data Bank (PDB) --
World Wide: -- USA:RCSB -- Japan:PDBj -- Europe:PDBe
PDB identification code examples:
- 1hho oxy-hemoglobin.
- 1d66 Gal4 transcriptional regulator bound to DNA.
- 104d DNA/RNA hybrid.
- 1bl8 potassium channel.
- 9ins insulin.
- Main page: green links connect text to molecular scenes.
- Molecules explained by users. Example:
X-Ray Crystallography and Resolution
Finding molecular models of interest
Each participant should find a molecule of personal interest.
Finding molecular models of interest:
Each person: please find a 3D model of a molecule related to your research or interests.
You will use the model that you select for the rest of the workshop.
- PDB code for an X-ray crystal structure with good resolution <= 2.5 Ångstroms.
- Has protein.
- Has ligand(s).
- Has a value for Rfree (free R).
If An Empirical Model Is Not Available
- Homology model. See
Limitations of Homology Modeling.
- Don't use a homology model if an empirical (X-ray or NMR) model exists for your protein. The empirical model will be more accurate. If unsure what to use, please ask the instructor.
How To Find Models:
Review of Protein Chemistry and Structure.
We'll do this quickly. The links are for participants who are educators.
DNA mRNA Protein.
DNA structure in Jmol
Estructura del ADN
20 Amino acids
Polypeptide chain geometry and steric restrictions
Covalent and non-covalent chemical bonds
- Codon = 3 nucleotides; 4 nucleotides3 =
Typical hydrogen bond
within a protein: hydrogen donor atom
is covalently bonded to hydrogen; acceptor
atom is not. In proteins, donor-acceptor distance
can be 2.5 to 3.5 Å.
Folding: hydrophobic collapse
cannot be reliably predicted
from sequence alone (using ab initio theory).
- Covalent bonds: lengths and angles nearly constant
- Non-covalent bonds: variable lengths and angles
Evolutionary Conservation: ConSurfDB & ConSurf
Enolase (4enl; a glycolytic enzyme)
Catalytic cleft is at the left.
Introduction to Evolutionary Conservation.
Identifying Functional Sites & Seeing Protein Evolution:
- Go to
Proteopedia.Org and enter 4enl in the search slot at left.
- Click the
load full button to load all atoms. (To improve performance, initially Proteopedia
loads only the alpha carbon atoms.)
- Look for Evolutionary Conservation and check the checkbox to color
each amino acid by evolutionary conservation.
- On the less conserved side of the molecule, touch the isolated highly conserved
residues to display the amino acid and sequence number.
Gly236 and Pro290 are highly conserved.
- Important: Many molecules do not have evolutionary conservation available in
Proteopedia. For these, and for homology models, you must calculate the conservation using
the ConSurf server.
- Go to the ConSurf Server.
Select Amino Acids.
Check YES there is a known protein structure.
Enter the PDB code, or upload your homology model.
Select a chain for analysis. ConSurf can analyze only one chain at a time.
Check NO, you will not be uploading a multiple sequence alignment. (ConSurf will create
one for you.)
Leave all parameters at their pre-set defaults.
(OPTIONAL: If you want a research grade result, check "Let me select the sequences for the analysis
manually out of BLAST results", and see
Limiting ConSurf Analysis to Proteins of a Single Function.)
Enter your email address at the bottom of the form (this is important so you don't lose
your results). Optionally enter a job title.
Click the button Submit.
It may take an hour or more to complete this calculation.
When it is finished, under Final Results, click the link View ConSurf Results with
FirstGlance in Jmol.
4enl result in ConSurf.
- ConSurf's Mechanism:
- Note the Caveats in
Proteopedia's Evolutionary Conservation.
- There are two ConSurf Servers:
NOT WORKING IN MAY, 2015
- Pre-calculated for every chain in the PDB.
- Results are shown in Proteopedia.
- Multiple Sequence Alignments typically include proteins of
more than one function, so some conservation may be hidden.
- Set up each job by hand.
- Easily select sequences for a single protein function, revealing
conservation (within a family of proteins performing
a single function) that may be hidden in ConSurfDB.
If you have a serious interest in the conservation in your protein,
- To start FirstGlance, go to
FirstGlance.Jmol.Org and enter the PDB code, or upload your homology model.
Unusually large models may take a long time to display and be sluggish to manipulate
in FirstGlance. For such cases, using Java will enable
much better performance in FirstGlance.
Java is not needed for most models. Ask the instructor for advice. Here are instructions for
Installing and Enabling Java.
- Explore 1izh in FirstGlance.
- Molecule Information Tab
- Year, Method.
- Free R.
- Chain details.
- Sequences: Crystallized vs. Full Length. Alignment at UniProt (1d66).
- Text contents of the PDB file.
- Views tab
- Top 3 rows of views:
Secondary Structure / Cartoon / N->C Rainbow
Composition / Hydrophobic/Polar / Charge..
Local Uncertainty / Vines / Thin Backbone
Ligands+ / Water / Slab
Hydrophobic core: Hydrophobic/Polar, then Slab.
Amphipathic helices and strands. (In FirstGlance,
use Isolate.. on each end of a helix or strand.)
- Compare with the Hydrophobic/Polar View of
- Resources tab
- See lipid bilayer boundaries (1bl8 or 7ahl).
Tools tab with Views.
- Salt bridges.
- Cation-pi interactions.
- Salt bridges in Charge View (Red sidechain touching
- Charges with Slab on.
- Sidechain distributions in Vines View (rings buried; charges on surface).
- Find (review Chart of AA): PHE, (VAL,LEU,ILE), ASN, THR
- Explore 9ins in FirstGlance.
- Tools tab
- Explore 3onz in FirstGlance. (Letter O not numeral zero!)
- Molecule Information Tab
- Two chains, not sequence identical.
- Missing residues.
- Ligands+ and non-standard residues
- Views tab
- Ligands button; smaller ligands.
- Hide (chain, toluene, isolated His).
- Tools tab
- Non-covalent interactions for HEM in chain A (blue chain).
- Resources tab
- Biological unit.
Introduction to Structural Bioinformatics and Genomics
Educators: You are welcome to use the slides linked below, or to adapt content from them into your own slides.
- Slides Covering:
- Why do we care about 3D macromolecular structure?
- What are 3D structure data?
- Where do 3D structure data come from?
- How much 3D structure knowledge do we have?
- What are the primary and derived 3D structure databases?
Animated Powerpoint Slides and Publication-Quality Images:
from Polyview-3D. Click on
the image for a
larger view and explanation.
Make Animated PowerPoint Slides and Publication-Quality
Images easily with
- Just fill out an easy form, submit it, and (shortly) voila!
Center and orient the molecule as you wish.
Coloring can be customized. Highlight residues that you specify.
Accepts PDB files obtained from ConSurf to color your figures or
slides by evolutionary conservation.
Once you have an animation from Polyview-3D:
- Windows Powerpoint: Simply drag the animation directly from the
Polyview-3D web page and drop it into a powerpoint slide.
- Mac OS X Powerpoint: (This works in Powerpoint:Mac 2008.)
Control-Click (Right-Click) on the animation in the Polyview-3D web page, and
select Save Image As ...
Save the image to the Desktop.
- Drag the image file (filename ending in .gif) from the Desktop and
drop it into a Powerpoint slide.
The animation will run only when the slide is projected.
We won't have time to go through the following resources in detail, so
the links and information below are provided mostly for you to use, if you wish, after the workshop.
Proteopedia.Org (Part II): Authoring
- Add Molecular Scenes and Content to
- Its a wiki: you or your students can add pages or customized
molecular scenes in Jmol.
- Great for
journal supplementary materials
research group websites
as well as
molecular structure tutorials
your pages from
being changed by anyone else, e.g.
- An easy Scene Authoring Tool attaches your customized
views to Green links.
- This is, by far, the easiest place to create molecular tutorials,
Nucleosomes (publically editable).
(enough for your entire class!) allow students to try
authoring temporary molecular scenes -- without individual accounts.
Screenshots can document student work.
Teaching Strategies Using Proteopedia.
Potassium channel (1R3J) showing membrane surface planes
- FirstGlance -> Resources Tab:
Orientations of Proteins in Membranes.
E. coli Porin 1HXX
- Compare with this theoretical model of a gramicidin channel in a phosphatidyl ethanolamine
FirstGlance in Jmol.
Be sure to toggle the Water and Ligand buttons!
(Thanks to S. Crouzy et al., Biophys. J. 67:1370-86, 1994.)
Jmol in Scientific Journals:
Interactive 3D Complements in Proteopedia:
- FirstGlance in Jmol: Look for the
Nature Structural and Molecular Biology.
- "Jmolized" Interactive 3D Journal Figures:
- Tutorials disponible en español at
MolviZ.Org (Estructura del ADN; Modelo de bicapa
lipídica y canal de gramicidina; Estructura del agua:
enlaces de hidrógeno)
BioModel (Estructura de proteínas; Glúcidos,
Lípidos, Vitaminas, Aminoácidos, Hélice alfa,
Hebra beta, Lisozima, Nucleósidos, ADN, ARN, et al.)
HighSchool.MolviZ.Org: Resources for High School Teachers.
- Molecular Workbench (from Concord Consortium):
Activities for High School Students with built-in assessment and reporting.
If this image is not moving, reload the page!
Morph of the lactose repressor bending DNA as it recognizes
Teaching Scenes, Tutorials, and Educators' Pages in Proteopedia, including Molecule of the Month.
- Teaching Strategies Using Proteopedia.
MolviZ.Org: Martz Central: Resources for High School, College, and Researchers.
- Bird Flu: N1 vs. Tamiflu Lesson Plan:
Animations / Morphs: Conformational Changes
(see MOVIE at right).
- Mutating your model:
Changing residue sidechains and rotamer minimization with
- DeepView beginners should start with the superb
Molecular Modeling for Beginners
by Gale Rhodes, Univ. Southern Maine.
- Structural Alignment of two or more chains or molecules, and how to view the alignment.
can align macromolecules
(one or more than one chains), selecting any subset of atoms for
the alignment (other atoms following), and retaining hetero
atoms. The results can be saved as a PDB file, but will need
manual editing to separate models with MODEL [N] and ENDMDL
records so that Jmol can distinguish the models.
Gale Rhodes provides a
DeepView tutorial: click on the section Comparing Proteins.
Structural Alignment Tools.
Keep in touch!