The view on the right is along the B-C bond with atom A placed at 12 o'clock. The Ramachandran plot A special way for plotting protein torsion angles was introduced by Ramachandran and co-authors and since then is called the Ramachandran plot.
The images below correspond to two different structures of the same protein. On the left is a structure at low resolution and on the right is a high-resolution structure. The Ramachandran plot shows the distribution of the torsion angles of a protein within certain regions. Many of the angle combinations, and therefore the conformations of residues, are not possible because of steric hindrance. By making a Ramachandran plot, protein structural scientists can determine which torsional angles are permitted and can obtain insight into the structure of peptides.
The scene on the right is the Ramachandran plot of ribonuclease H. Two common examples of secondary structure are illustrated below. When viewing the helix on end, observe the open center of the helix.
Since the 's, great expansion in the number and quality of macromolecular crystal structures and advances in methodology have greatly improved understanding of the energetically favored, allowed, and truly disallowed conformations of proteins and nucleic acids. On the Rama Plot, find the dot for the center residue. Click and drag the dot around on the diagram while watching the model stereo recommended.
You are changing phi when you drag it horizontally, and psi when you drag it vertically. This allows you to adjust backbone conformations during model building. You can undo a single change with Edit: Undo.
To modify phi only, hold down the 9 key while dragging; to modify psi only, hold down 0 the number zero while dragging. Now review the definitions of phi and psi above , and use the Rama plot to confirm that the torsional angles you are changing correspond to those described in the definitions. What is the relationship -- cis or trans -- between the first and last atoms defined by each angle when the value of the angle is zero?
When the angle is ? For either phi or psi, set the angle near zero. Look along the bond that rotates when you move the dot, with the fixed end pointing toward you and the moving end pointed away looking toward the C-terminus, or toward higher numbered residues.
What direction of rotation of the moving end corresponds to a positive rotation? Answers below. When you change backbone angles, the N-terminal part of the model is fixed, and the C-terminal end moves.
You can allow the N-terminal part to move instead by clicking the small C in the upper left corner of the Ramachandran Plot window, just the below the Help? Try it. Clicking changes C to N. When N is showing, the N-terminal end moves and the C-terminal end is fixed. Again select, display, and center three adjacent residues. Look at their conformation, as well as the position of their Rama dots, before proceeding.
K: Modeling of globular proteins. Ramakrishnan C, Ramachandran GN: Stereochemical criteria for polypeptide and protein chain conformations. Allowed conformations for a pair of peptide units. Biophys J , 5: — Biopolymers , — Nucleic Acids Research , — Protein Sci , 8: — Journal of Physical Chemistry , B — Article Google Scholar. Phi-psi maps for N-acetyl alanine N'-methyl amide: comparisons, contrasts and simple experimental tests.
J Biomol Struct Dyn , 7: — O hydrogen bonds in proteins. O, C-H N, and C-H Cl hydrogen bonds. J Am Chem Soc , — O hydrogen bonds in the coordination of water molecules. Analysis of Neutron Diffraction Data. Bhattacharyya R, Chakrabarti P: Stereospecific interactions of proline residues in protein structures and complexes. J Mole Biol , 4 — Download references. You can also search for this author in PubMed Google Scholar. Correspondence to Bosco K Ho. Both authors conceived the study.
BKH carried out the data analysis and modelling, and drafted the manuscript. RB provided guidance and mentorship. Reprints and Permissions. Ho, B. The Ramachandran plots of glycine and pre-proline. BMC Struct Biol 5, 14 Download citation. Received : 15 March Accepted : 16 August Published : 16 August Anyone you share the following link with will be able to read this content:. Sorry, a shareable link is not currently available for this article. Provided by the Springer Nature SharedIt content-sharing initiative.
Skip to main content. Search all BMC articles Search. Download PDF. Abstract Background The Ramachandran plot is a fundamental tool in the analysis of protein structures. Conclusion We have identified the specific interactions that affect the backbone of glycine and pre-proline.
0コメント