Kinesin Esthetics - Famous Proteins in Frames

Back to the Thought Deposit - Takaisin Ajatusvarikolle
→ CHALLENGE - HAASTE←
DINOGLYFS - DINOGLYFIT - Prehistoric creatures documented by the ancient man - Esihistorialliset eläimet historian lehdillä

Art Resolutionism

Resolutionismi-taidesuuntaus

Famous Proteins

Structure Archives

from PDB, Protein Data Bank

KINESIN

KINESIINI

Note! The image is a stereo pair - You should adjust Your eyes.

Rotation of the stalk/neck and one head of the kinesin motor protein, Ncd: 1N6M

Coordinates from

Yun, M., Bronner, C.E., Park, C.-G., Cha, S.-S., Park, H.-W., Endow, S.A. (2003)

Rotation of the stalk/neck and one head in a new crystal structure of the kinesin motor protein, Ncd

EMBO J. 22: 1-8

http://www.rcsb.org/pdb/explore/explore.do?structureId=1N6M

Downloaded from PDB (Protein Data Bank) or PSI (Protein Structure Initiative)

Created by PyMol, Python-enhanced molecular graphics tool: http://pymol.sourceforge.net/

PyMol excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories.

It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!

Operating System : All 32-bit MS Windows (95/98/NT/2000/XP), All POSIX (Linux/BSD/UNIX-like OSes), Linux, OS X, Solaris, SGI IRIX

Programming Language : C, Python, Tcl

License : Python License (CNRI Python License)

PyMOL is an open-source, user-sponsored, molecular visualization system created by Warren Lyford DeLano and commercialized by DeLano Scientific LLC, which is a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is well suited to producing high quality 3D images of small molecules and biological macromolecules such as proteins. According to the author, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. PyMOL is one of few open source visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language.

PyMOL Wiki

DeLano Scientific LLC

Protein alignment program coupled with PyMOL

Molecular movie-making with PyMOL

Example of PyMol-made 3D ANIMATION of 48% W/W glycoprotein with modelled carbohydrate (sugar) residues:

bi061657lsi20060817_083904.qt (12472 K)

http://pubs3.acs.org/acs/journals/supporting_information.page?in_manuscript=bi061657l

Ojala PJ, Hermansson M, Tolvanen M, Polvinen K, Hirvonen T, Impola U, Jauhiainen M, Somerharju P, Parkkinen J.

Biochemistry; 2006; 45(47) pp 14021 - 14031

"Identification of Alpha-1 Acid Glycoprotein as a Lysophospholipid Binding Protein:

A Complementary Role to Albumin in the Scavenging of Lysophosphatidylcholine"