6BBB0333
L17 & 18 – Molecular Dynamics Simulations of Proteins
Conformational changes in the enzyme Triosephosphate Isomerase
Enzyme structures change for activation
- Catalytic activity depends on opening of substrate binding sites.
- Enzymes need to switch between active and inactive states, often these are
open and closed structures
-
- Enzymes have active and inactive form – must be activated
- These forms are induced via structural changes
- TIM (Triosephosphate Isomerase) is a well-studied enzyme, with high activity
exhibiting an open and closed state.
- TIM has open and closed state
o These states are well characterized by the loop regions
o Loops undergo structural changes to switch between states
o Very flexible structure that moves around
- i.e. dynamical process that is required for function (this change is needed to
observe function of enzyme)
Allosteric Regulation of Function
Allosteric regulation
- Binding of ligand to a site distant to the active site, the so called allosteric site,
changes the structure of the protein.
- This change enables substrate binding at the active site.
,6BBB0333
Hemoglobin shows allostery
- There are four oxygen binding site in hemoglobin (tetrameric arrangement).
- Binding of one oxygen molecule reshapes structure (of all binding sites),
facilitating oxygen binding in the remaining sites.
- These are significant changes
o We are not changing the secondary structure but the 3D arrangement
is quite different
o Atoms somehow know what change to make and where to move
(happens cooperatively)
, 6BBB0333
Muscle Proteins and Limits of Experimental Resolution
- How can we study the dynamic nature of the interactions between actin and
myosin?
- Can observe this motion using sliding filament assay
- We can build an assay with reduce complexity known as sliding filament
assay. With it we can easily observe the movement of actin filaments via
“contractions”.
- The setup allows easy changes of many parameters e.g. pH, salt, ATP/ADP,
proteins, mutations etc.
o To see what kind of conditions are needed to observe something
- Set up:
o Myosin monomers on surface
o Filaments of surface that can slide around and interact
- Proteins MOVE – they are not static
Sliding Filament Assays
- We can play around with parameters and test the impact of changes on actin
motions, but nonetheless the system is still very complex.
- We do not see any structural detail in the experimental setup - just some
fluorescent blobs moving around. (we don’t know what facilitates these
motions and how they occur) – need simulations!
- Simulations are very well placed to bring together the macroscopic
observations from such assays with the microscopic information from the
structures of the involved proteins
L17 & 18 – Molecular Dynamics Simulations of Proteins
Conformational changes in the enzyme Triosephosphate Isomerase
Enzyme structures change for activation
- Catalytic activity depends on opening of substrate binding sites.
- Enzymes need to switch between active and inactive states, often these are
open and closed structures
-
- Enzymes have active and inactive form – must be activated
- These forms are induced via structural changes
- TIM (Triosephosphate Isomerase) is a well-studied enzyme, with high activity
exhibiting an open and closed state.
- TIM has open and closed state
o These states are well characterized by the loop regions
o Loops undergo structural changes to switch between states
o Very flexible structure that moves around
- i.e. dynamical process that is required for function (this change is needed to
observe function of enzyme)
Allosteric Regulation of Function
Allosteric regulation
- Binding of ligand to a site distant to the active site, the so called allosteric site,
changes the structure of the protein.
- This change enables substrate binding at the active site.
,6BBB0333
Hemoglobin shows allostery
- There are four oxygen binding site in hemoglobin (tetrameric arrangement).
- Binding of one oxygen molecule reshapes structure (of all binding sites),
facilitating oxygen binding in the remaining sites.
- These are significant changes
o We are not changing the secondary structure but the 3D arrangement
is quite different
o Atoms somehow know what change to make and where to move
(happens cooperatively)
, 6BBB0333
Muscle Proteins and Limits of Experimental Resolution
- How can we study the dynamic nature of the interactions between actin and
myosin?
- Can observe this motion using sliding filament assay
- We can build an assay with reduce complexity known as sliding filament
assay. With it we can easily observe the movement of actin filaments via
“contractions”.
- The setup allows easy changes of many parameters e.g. pH, salt, ATP/ADP,
proteins, mutations etc.
o To see what kind of conditions are needed to observe something
- Set up:
o Myosin monomers on surface
o Filaments of surface that can slide around and interact
- Proteins MOVE – they are not static
Sliding Filament Assays
- We can play around with parameters and test the impact of changes on actin
motions, but nonetheless the system is still very complex.
- We do not see any structural detail in the experimental setup - just some
fluorescent blobs moving around. (we don’t know what facilitates these
motions and how they occur) – need simulations!
- Simulations are very well placed to bring together the macroscopic
observations from such assays with the microscopic information from the
structures of the involved proteins
