MACROMOLECULAR STRUCTURE
PROTEINS AND NUCLEIC ACIDS
(revision 10-21-2016)
Author: Loren Dean Williams, Georgia Tech
This page and the information contained on it are intended to facilitate the incorporation of 3D structures and their visualization into the teaching of biochemistry and biophysics. Others can copy, distribute, display, and make derivative works for non-commercial purposes, so long as attribution is given.
Initial development support provided by the NSF CAREER Program
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Topic

Subject
1
Background
Enthalpy, entropy and free energy
2
Molecular Interactions
Web Site
-----------------------------------> Water Pymol Script
-----------------------------------> GC Base Pair Pymol Script
-----------------------------------> Short Range Repulsion Pymol Script
Ions
-----------------------------------> Electrostatic Interactions Pymol Script
The hydrophobic effect
Small molecule library
3
Protein monomers and oligomers
Amino acids
The peptide bond
-----------------------------------> Peptide Bond Pymol Script
Φ/Ψ torsion angles
-----------------------------------> Φ/Ψ Pymol Script
4
Protein secondary structure
α-Helix
-----------------------------------> α-Helix Pymol Script
β-Sheet
-----------------------------------> Parallel β-Sheet Pymol Script
-----------------------------------> Antiparallel β-Sheet Pymol Script
Loops and turns
5
Protein Folds
-----------------------------------> Protein Folds Pymol Script
Fibrous proteins
-----------------------------------> Collagen Pymol Script

α-Helical proteins
-----------------------------------> Albumin Pymol Script
-----------------------------------> Myoglobin Pymol Script
-----------------------------------> Hemoglobin Pymol Script
-----------------------------------> Seven Transmembrane α-Helices Pymol Script
α-Helical/β-Sheet proteins
-----------------------------------> Carboxypeptidase Pymol Script
-----------------------------------> Ribonuclease A Pymol Script
Anti-parallel β-sheet proteins
-----------------------------------> Porin Pymol Script
-----------------------------------> Amyloid Pymol Script
parallel β-sheet proteins
-----------------------------------> HMW1 Adhesin Pymol Script
-----------------------------------> Groel
-----------------------------------> Evolution of Folding
6
Protein/Metal Interactions
Metals (radii, coordinate numbers, etc)
-----------------------------------> Calmodulin Pymol Script
Potassium Channel
7
Protein/Nucleotide Interactions
Rossman Fold
8
Bases, Nucleosides and Nucleotides
ribose/deoxyribose
-----------------------------------> Syn/Anti Pymol Script
-----------------------------------> Sugar Pucker Pymol Script
bases
base pairs, triplets and quartets
----------------------------------> Hoogsteen Base Pair Pymol Script
9a
DNA Structure
-----------------------------------> B-Form DNA Pymol Script
-----------------------------------> Quadruplex DNA Pymol Script
phosphodiester backbone
-----------------------------------> DNA Torsion Angle Pymol Script
-----------------------------------> Triplex Pymol Script
A,B,Z conformation
Supercoiling
9b
RNA Structure
-----------------------------------> ATP Pymol Script
-----------------------------------> A-Form RNA Pymol Script
GNRA Tetraloops
-----------------------------------> GNRA Tetraloop Pymol Script
---------------------------------------------> coordinates for 20 GNRA tetraloops
Kink-Turns
-----------------------------------> Kink-Turn Pymol Script
tRNA
-----------------------------------> tRNA Pymol Script
Ribosome
-----------------------------------> Small Subunit Pymol Script
-----------------------------------> Thermus Thermophilus Ribosome Pymol Script
motifs
10
Interactions of nucleic acids with small molecules
Water
-----------------------------------> Spine of Hydration Pymol Script
Magnesium
Spermine
Minor groove binders
Intercalators and Bis-intercalators
11a
Carbohydrate
Images and Coordinates
----------------------------------->Cellulose Pymol Script
11b
Interactions of nucleic acids with proteins
----------------------------------->Toll-like Receptor Pymol Script
-----------------------------------> HU Protein Pymol Script
-----------------------------------> DNA Ligase Pymol Script
Nucleosome
-----------------------------------> Nucleosome Pymol Script
-----------------------------------> P22 Repressor: HTH Pymol Script
-----------------------------------> TBP Pymol Script
-----------------------------------> Yeast RNA Pol II Pymol Script
Zinc Fingers
-----------------------------------> Zinc Finger Pymol Script
ZIP
Helix-loop-helix
β-ribbon
Restriction and Modification Enzymes
-----------------------------------> Bam HI Pymol Script
-----------------------------------> BGL II Pymol Script
-----------------------------------> Eco RI Pymol Script
-----------------------------------> Fok I Pymol Script
-----------------------------------> Not I Pymol Script
-----------------------------------> Pvu II Pymol Script
tRNA synthetases
-----------------------------------> Class I: Glutamyl-tRNA sythetase Pymol Script
Rev response element/rev peptide
Polymerases
----------------------------------->
Bacillus DNA Polymerase I Pymol Script
11c
Viruses & Phages
----------------------------------->QΒ VLP Pymol Script
12
Enzymes and Catalysis
Serine Proteases
-----------------------------------> Trypsin TS Analog Pymol Script
-----------------------------------> Hexokinase Pymol Script
-----------------------------------> Succinyl-CoA Synthetase Pymol Script
-----------------------------------> Amidoribosyl Transferase Pymol Script
13
Databases
PDB, CSD, PubMed
How to use the PDB
14
Display and Manipulation
Student Pymol Download Mac PC Pymol Documentation

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