Graphical abstract template · Drug discovery & proteins · Protein folding
Protein folding: the energy landscape
Why a chain finds its fold: a random search would take forever (Levinthal), but the energy landscape is a funnel with many downhill routes to one native state, the free-energy minimum that the sequence sets (Anfinsen). With the backbone angles of the native state, a free-energy surface and a molecular dynamics box.
Updated 5 cited papers49 editable layers
At a glance
- Category
- Drug discovery & proteins
- Method
- Protein folding
- Starting materials
- An unfolded polypeptide chain
- Product
- The native fold, the free-energy minimum
- Key result
- Landscapes, angles and the surface are schematic or synthetic examples
- Figure
- 1920 × 1080 px (16:9), 49 editable layers, 6 generated objects
Step by step
- The sequence decidesThe native structure is set by the amino acid sequence (Anfinsen 1973)
- No blind searchA golf-course landscape has no slope to follow; a funnel has many routes downhill (Dill & Chan 1997)
- TrapsMisfolded intermediates can hold a chain up on the way down
- Backbone anglesFolded residues sit in the helix and sheet regions of the Ramachandran plot (Ramachandran 1963)
- SimulationMolecular dynamics follows the atoms in a box of water (Karplus & McCammon 2002)
Strengths
- Explains fast folding without a single pathway
- One picture for folding, misfolding and design
Limitations
- Real landscapes are high-dimensional; drawings project them onto two or three axes
Uses
- Teaching
- Folding and misfolding studies
- Simulation figures
Papers this template follows
- Anfinsen, “Principles that govern the folding of protein chains”, Science 1973. doi:10.1126/science.181.4096.223primary
- Dill & Chan, “From Levinthal to pathways to funnels”, Nat. Struct. Biol. 1997. doi:10.1038/nsb0197-10primary
- Ramachandran, Ramakrishnan & Sasisekharan, “Stereochemistry of polypeptide chain configurations”, J. Mol. Biol. 1963. doi:10.1016/S0022-2836(63)80023-6method origin
- Karplus & McCammon, “Molecular dynamics simulations of biomolecules”, Nat. Struct. Biol. 2002. doi:10.1038/nsb0902-646further reading
- Pauling, Corey & Branson, “The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain”, PNAS 1951. doi:10.1073/pnas.37.4.205further reading
After Anfinsen, Science 1973 (doi:10.1126/science.181.4096.223), Dill & Chan, Nat. Struct. Biol. 1997 (doi:10.1038/nsb0197-10), Ramachandran et al., J. Mol. Biol. 1963 and Karplus & McCammon, Nat. Struct. Biol. 2002. Landscapes, angles and the free-energy surface are synthetic.
How templates are written and checked: editorial guidelines.
Questions
What does the “Protein folding: the energy landscape” template show?
Why a chain finds its fold: a random search would take forever (Levinthal), but the energy landscape is a funnel with many downhill routes to one native state, the free-energy minimum that the sequence sets (Anfinsen). With the backbone angles of the native state, a free-energy surface and a molecular dynamics box.
What are the steps shown in “Protein folding: the energy landscape”?
1. The sequence decides: The native structure is set by the amino acid sequence (Anfinsen 1973). 2. No blind search: A golf-course landscape has no slope to follow; a funnel has many routes downhill (Dill & Chan 1997). 3. Traps: Misfolded intermediates can hold a chain up on the way down. 4. Backbone angles: Folded residues sit in the helix and sheet regions of the Ramachandran plot (Ramachandran 1963). 5. Simulation: Molecular dynamics follows the atoms in a box of water (Karplus & McCammon 2002).
What are the starting materials and the product?
Starting materials: An unfolded polypeptide chain. Product: The native fold, the free-energy minimum.
Which papers is “Protein folding: the energy landscape” based on?
Anfinsen, “Principles that govern the folding of protein chains”, Science 1973 (doi:10.1126/science.181.4096.223); Dill & Chan, “From Levinthal to pathways to funnels”, Nat. Struct. Biol. 1997 (doi:10.1038/nsb0197-10); Ramachandran, Ramakrishnan & Sasisekharan, “Stereochemistry of polypeptide chain configurations”, J. Mol. Biol. 1963 (doi:10.1016/S0022-2836(63)80023-6); Karplus & McCammon, “Molecular dynamics simulations of biomolecules”, Nat. Struct. Biol. 2002 (doi:10.1038/nsb0902-646); Pauling, Corey & Branson, “The structure of proteins: two hydrogen-bonded helical configurations of the polypeptide chain”, PNAS 1951 (doi:10.1073/pnas.37.4.205).
Can I edit the “Protein folding: the energy landscape” template?
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