ATP and GAP Binding Affinity Quiz

A measure of the concentration of a ligand (like ATP or GAP) needed to achieve half-maximal binding to a protein.

The Hill coefficient describes the cooperativity of binding. A value greater than 1 indicates positive cooperativity, meaning binding of one ligand increases the affinity for subsequent ligands.

The concentration of ATP required to achieve half-maximal binding to the protein in this study.

The concentration of GAP required to achieve half-maximal binding to the protein in this study.

The protein under investigation binds ATP and GAP with different affinities, as indicated by their distinct KD values.

A part of a protein that can move or change conformation, often involved in interactions with other molecules.

The space within a cell where many biochemical reactions occur.

A region within a cell where proteins are synthesized and folded.

A region within a cell where proteins are sorted and packaged for export.

The movement of a molecule from one location to another within a cell.

The process by which a protein changes its shape or conformation.

An ion that has a positive charge.

An ion that has a negative charge.

The addition of a cation or anion to a solution can affect the movement of proteins within a cell.

Loop 5 is a specific region of a protein that plays a role in its translocation across a cell membrane.

The simultaneous addition of GAP and Mg2+ to the OEP21 - MANT-ATP complex decreased the IC50 values for both OEP21 constructs to ~1 mM. This indicates that GAP and Mg2+ synergistically facilitate ATP dissociation from OEP21.

The KD values for ATP determined with a set of OEP21 variants all lie within 50% of the value obtained with the wild-type (WT) protein. This implies that the removal or shifting of individual positive charges can be compensated by other positively charged side chains in close proximity.

The binding affinity of ATP in the presence of Mg2+ is weaker compared to ATP alone.

Inorganic phosphate also dissociated the OEP21-ATP complex with an IC50 value of ~10 mM, which is a higher concentration than GAP and Mg2+.

The high phosphate concentration (1 to 10 mM) observed in plant cells is similar to the concentration required for ATP dissociation from OEP21.

GAP binds weakly to detergent micelles due to partial unspecific binding.

Mg2+ has a strong affinity for ATP (50 µM) but interacts only weakly with GAP or phosphate (~9 mM each).

Phosphorylated metabolites like ATP, GAP, and phosphate utilize the same positively charged binding surface of OEP21.

The mechanism by which OEP21 interacts with metabolites, particularly those with a high affinity for its pore, is not specific to a particular molecule but rather relies on the overall electrostatic properties of the molecule.

The electrostatic charge of the molecule is important, with OEP21 showing significantly reduced binding affinity for GAP (a primary product of photosynthesis ) and ATP when their negative charge density is lowered due to increased NaCl or MgCl2 concentrations.

The OEP21 pore exhibits a high affinity to ATP but its binding is strongly influenced by the concentration of salts such as NaCl and MgCl2.

A loop (L5) located within the OEP21 pore is a crucial factor in the interaction with GAP, slowing down its translocation through the pore.

Removal of the L5 loop from OEP21 (OEP21ΔL5) significantly increases the translocation frequency of GAP, indicating that L5 is a significant bottleneck.

Computational simulations, involving molecular dynamics, are used to analyse the movements of GAP as it translocates across the OEP21 channel.

The positive charges on OEP21 are crucial for the interaction with GAP, as GAP moves along these charges during its translocation through the pore.

An artificial electric field is applied in computational models to facilitate the translocation of GAP through the OEP21 pore during simulations.

A type of protein structure that is flexible and changes over time, often associated with proteins that perform dynamic functions.

A specific region on a protein known as L5, which exhibits flexibility and is affected by the presence of ATP.

ATP, or adenosine triphosphate, is a key energy molecule in cells. When added to the protein OEP21, ATP interacts with it and causes a change in the protein's structure.

A technique used to study the structure of molecules. Nuclear Magnetic Resonance (NMR) spectroscopy measures the magnetic properties of atoms within a molecule, providing insights into the molecule's structure.

A technique used to measure the interactions between protons in a molecule. Nuclear Overhauser Effect (NOE) helps to identify close proximity between atoms within a molecule.

A technique used to study the location of amino acids within a protein structure.

A technique that uses chemicals to crosslink different parts of a protein. This helps to determine which parts of a protein are close together and helps to understand its structure.

A chemical that can cause a protein to unravel, losing its defined structure.

A protein called OEP21 that regulates the movement of lipids between different compartments within the chloroplast.

A type of protein that has the ability to break down other proteins.

A state where a protein is not folded into its proper shape.

A condition where a protein has multiple copies of itself joined together.

The distance between two points on a protein structure, measured in parts per million (ppm) using NMR spectroscopy.

The strength of the interaction between two molecules, in this case, ATP and the protein, is measured by the dissociation constant (KD). A fold increase in KD means that the interaction between the protein and ATP is weakened, making it easier for them to separate.

This refers to the ratio of the concentrations of ATP and the protein. A 1:1 molar ratio means that there is an equal amount of ATP and protein in the solution.

Excess ATP means that there is a much larger amount of ATP than the protein in the solution.

This is the protein studied in the experiment, denoted by "T". It interacts with ATP.

These are the specific regions on the protein T that interact with ATP. The numbers indicate different locations on the protein structure.

These symbols represent different amino acids in the protein structure. A = alanine, W = tryptophan, N = asparagine, R = arginine. This indicates the specific amino acids involved in the binding of ATP.

This represents the change in length (∆L) of the protein T after binding to ATP.

This shows the fold increase in KD for ATP. This tells us how much weaker the interaction between ATP and the protein becomes under different conditions.

This indicates the relative amount of ATP used in the experiment. Rel. >1 means that more than one ATP molecule was used.

This refers to the angle of separation between protein T and ATP. 90° implies that the protein and ATP are perpendicular to each other.

This indicates the location of the protein T in the experiment. The protein T is positioned at the center of the experiment, with ATP binding to it from the left.

These represent the specific amino acids on the protein T that are responsible for interacting with ATP. The numbers indicate the specific locations on the protein.

This represents the protein T in different conformations, meaning different shapes that the protein can adopt. These conformations could be influenced by factors like the presence or absence of ATP.

This indicates that the fold increase in KD is greater than 1, meaning the interaction between the protein and ATP is weakened. The arrow indicates the direction of the increase in KD.

These are graphical representations showing the relationship between different experimental variables. The height of the bars indicates the value of a specific variable.