Structural Basis of Sequential and Concerted Cooperativity
Abstract
:1. Introduction
2. Materials and Methods
3. Results
3.1. Human Hemoglobin
3.2. Aspartate Transcarbamylase
3.3. Phosphofructokinase
3.4. Glycogen Phosphorylase
3.5. The Chemotactic Asp Receptor from S. typhimurium and E. coli
3.6. Asp Semialdehyde Dehydrogenase
3.7. Bacterial D-Lactate Dehydrogenases
3.8. Bacterial Purine Nucleoside Phosphorylase
3.9. Other Enzymes Obeying a Sequential Reaction Mechanism
4. Conclusions
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Concerted Models | Sequential Models | |
---|---|---|
tertiary structure symmetry (all subunits share or do not share the same tertiary structure in the various ligation states) | necessary for unliganded, partially liganded and fully liganded states (asymmetry within T may be tolerated) | necessary asymmetry of ligation intermediates; asymmetry in the liganded state is tolerated |
quaternary conformation equilibrium in the absence of the ligand | necessary, for all ligation intermediates, described by the allosteric constant L (see Equation (2)). | absent (see Equation (1)) |
cooperativity in the absence of quaternary structure change | impossible | possible |
positive homotropic cooperativity | possible | possible |
negative homotropic cooperativity | usually impossible (some exceptions may be considered) | possible |
heterotropic regulation | almost always present | possible but not common |
quaternary enhancement/constraint | usually quaternary constraint (but enhancement possible) | both possible |
structural differences between the fully liganded and fully unliganded states | present (the main difference occurs between the R and T state, irrespective of ligation) | present |
Protein | Reaction Mechanism | Available Information |
---|---|---|
vertebrate hemoglobins | concerted | -positive homotropic cooperativity -ligand-independent allosteric equilibrium -symmetry of ligation intermediates -absence of cooperativity under conditions that prevent the quaternary structure change -quaternary constraint |
Asp transcarbamylase | concerted | -positive homotropic cooperativity -ligand-independent allosteric equilibrium -quaternary constraint |
Phosphofructokinase | likely concerted | -positive homotropic cooperativity -quaternary enhancement -T state is only induced by heterotropic effector (s) -Ligand binds only to the R state |
Glycogen phosphorylase B | likely concerted | -positive homotropic cooperativity |
Bacterial Asp receptor | sequential | -negative homotropic cooperativity -asymmetry of ligation intermediates |
dTMP synthase | sequential | -negative homotropic cooperativity -asymmetry of ligation intermediates |
Asp semialdehyde dehydrogenase | sequential | -negative homotropic cooperativity -asymmetry of ligation intermediates |
Bacterial D-Lactate dehydrogenases | sequential | -negative or positive homotropic cooperativity -strong asymmetry in either the liganded or unliganded state |
Bacterial Purine nucleoside phosphorylase | sequential | -negative homotropic cooperativity -strong asymmetry in the liganded state |
Ligation State RMSD | |
---|---|
Human Hemoglobin (Concerted, MWC-like) | |
R Hb(CO)4, PDB 2DN3, vs. T Hb, PDB 2DN2 | tertiary, average: 0.67 Å overall (tertiary + quaternary): 2.43 Å |
α1 subunit in T Hb, PDB 2DN2, vs. α2 subunit in THb, PDB 2DN2 | tertiary: 0.23 Å |
β1 subunit in T Hb, PDB 2DN2, vs. β2 subunit in T Hb, PDB 2DN2 | tertiary: 0.3 Å |
R Hb(CO)4, PDB 2DN3, vs. T αFeCO2 βCo2, PDB 1COH | tertiary, average: 0.67 Å |
R Hb(O2)4, PDB 2DN1, vs. THb(O2)4, PDB 1GZX | overall (tertiary + quaternary): 2.57 Å |
T Hb, PDB 2DN2, vs. T Hb(O2)4, PDB 1GZX | tertiary, α subunits: 0.28 Å tertiary, β subunits: 0.41 Å overall (tertiary + quaternary): 0.51 Å |
E. coli Asp transcarbamylase (concerted, MWC-like) | |
Unliganded T ATC, PDB 6AT1 vs. PALA-liganded R ATC, PDB 8ATC | tertiary (catalytic subunits): 1.85 Å tertiary (regulatory subunits): 1.70 Å overall (tertiary + quaternary): 6.20 Å |
Unliganded T ATC, PDB 6AT1 vs. unliganded T ATC, PDB 6AT1 | tertiary (catalytic subunits): 0.56 Å tertiary (regulatory subunits): 1.34 Å |
PALA-liganded R ATC, PDB 8ATC vs. PALA-liganded R ATC, PDB 8ATC | tertiary (catalytic subunits): 0.32 Å tertiary (regulatory subunits): 1.43 Å |
Geobacillus stearothermophylus phosphofructokinase (concerted, MWC-like ?) | |
PGC-inhibited T PFK, PDB 6PFK, vs. unliganded R PFK, PDB 3PFK | tertiary, average: 0.94 Å overall (tertiary + quaternary): 1.55 Å |
PGC-inhibited T PFK, PDB 6PFK, vs. PGC-inhibited T PFK, PDB 6PFK | tertiary, average: 0.28 Å |
Rabbit (O. cuniculus) muscle glycogen phosphorylase b (concerted, MWC-like ?) | |
R GPb, PDB 7GPB vs. T GPb, PDB 8GPB | tertiary, average: 1.33 Å overall (tertiary + quaternary): 2.61 Å |
R GPb, PDB 7GPB vs. R GPb, PDB 7GPB | tertiary, average: 0.55 Å |
S. typhimurium Asp receptor (sequential, KNF-like) | |
unliganded, PDB 1LIH vs. liganded, PDB 2LIG | tertiary 1LIH vs. 2LIG A: 2.58 Å tertiary 1LIH vs. 2LIG B: 2.42 Å overall (tertiary + quaternary): 2.85 Å |
liganded, PDB 2LIG A (high affinity), vs. liganded, PDB 2LIG B (low affinity) | tertiary: 2.44 Å |
E. coli Asp semialdehyde dehydrogenase (sequential, KNF-like) | |
unliganded, PDB 1GL3, vs. half-liganded, PDB 1T4B | tertiary, liganded subunit of 1T4B: 1.3 Å tertiary, unliganded subunit of 1T4B: 0.94 Å overall (tertiary + quaternary): 1.49 Å |
unliganded, PDB 1GL3, vs. unliganded, PDB 1GL3 | tertiary: 0.27 Å |
half-liganded, PDB 1T4B, vs. half-liganded, PDB 1T4B | tertiary: 0.62 Å |
P. aeruginosa D-lactate dehydrogenase (sequential, KNF-like) | |
unliganded PDB 6ABJ, vs. liganded PDB 5Z20 | tertiary (average): 2.35 Å overall (tertiary + quaternary): 3.30 Å |
unliganded PDB 6ABJ, vs. unliganded PDB 6ABJ | tertiary (average): 0.31 Å |
liganded PDB 5Z20, vs. liganded PDB 5Z20 | tertiary (average): 0.50 Å |
F. nucleatum D-lactate dehydrogenase (sequential, KNF-like) | |
unliganded PDB 6ABI, vs. liganded PDB 5Z21 | tertiary (average): 4.7 Å overall (tertiary + quaternary): 6.44 Å |
unliganded PDB 6ABI, vs. unliganded PDB 6ABI | tertiary (average): 1.9 Å |
liganded PDB 5Z21, vs. liganded PDB 5Z21 | tertiary (average): 0.25 Å |
E. coli purine nucleoside phosphorylase (sequential, KNF-like) | |
unliganded, PDB 1ECP, vs. fully liganded, PDB 1A69 | tertiary (average) 0.88 Å tertiary (open vs. open) 0.31 Å tertiary (open vs. closed) 1.0–1.32 Å overall (tertiary + quaternary) 0.84 Å |
unliganded, PDB 1ECP, vs. partially liganded, PDB 4TTA | tertiary (average) 1.3 Å tertiary (open vs. open) 0.47 Å tertiary (open vs. closed) 1.37 Å tertiary (open vs. destructured) 2.75 Å overall (tertiary + quaternary) 1.50 Å |
fully liganded, PDB 1A69, vs. partially liganded, PDB 4TTA | tertiary (average) 1.44 Å tertiary (open vs. open) 0.45 Å tertiary (open vs. closed) 1.5 Å tertiary (closed vs. destructured) 3.5 Å tertiary (open vs. destructured) 2.75 Å overall (tertiary + quaternary) 1.71 Å |
unliganded, PDB 1ECP, vs. unliganded, PDB 1ECP | tertiary (average) 0.32 Å |
fully liganded, PDB 1A69, vs. fully liganded, PDB 1A69 | tertiary (average) 1.35 Å tertiary (A-closed vs. B-open) 1.32 Å tertiary (A-closed vs. C-open) 1.76 Å tertiary (B-open vs. C-open) 0.98 Å |
partially liganded, PDB 4TTA, vs. partially liganded, PDB 4TTA | tertiary (A-closed vs. F-closed) 0.17 Å tertiary (B-open vs. D-open) 0.45 Å tertiary (A/F-closed vs. B/D-open) 1.39 Å tertiary (A/F-closed vs. E-destruct.) 3.52 Å tertiary (B/D-open vs. E-destruct.) 2.82 Å |
Protein | Reaction Scheme | R1 | R2 | R3 |
---|---|---|---|---|
human HbA (2DN2/2DN3) | concerted | 0.28 | 0.11 | 0 |
E. coli ATC (6AT1/8ATC) | concerted | 0.28 | 0.09 * | 0.05 * |
G. stearothermophyilus PFK (6PFK/3PFK) | likely concerted | 0.60 | 0.18 | 0 |
rabbit glycogen phosphorylase b (7GPB/8GPB) | likely concerted | 0.51 | 0 | 0.21 |
S. typhimurium Asp receptor (1VLT/1VLS) | sequential | 0.88 | 0 | 0.85 |
E. coli Asp semialdehyde dehydrogenase (1T4B/1GL3) | sequential | 0.75 | 0.18 | 0.42 |
Pseudomonas aeruginosa D-lactate dehydrogenase (6ABJ/5Z20) | sequential | 0.71 | 0.09 | 0.15 |
Fusobacterium nucleatum D-lactate dehydrogenase (6ABI/5Z21) | sequential | 0.73 | 0.29 | 0.04 |
E. coli purine nucleotide phosphorylase (1ECP/1A69) | sequential | 1.05 | 0.38 | 1.60 |
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Morea, V.; Angelucci, F.; Tame, J.R.H.; Di Cera, E.; Bellelli, A. Structural Basis of Sequential and Concerted Cooperativity. Biomolecules 2022, 12, 1651. https://doi.org/10.3390/biom12111651
Morea V, Angelucci F, Tame JRH, Di Cera E, Bellelli A. Structural Basis of Sequential and Concerted Cooperativity. Biomolecules. 2022; 12(11):1651. https://doi.org/10.3390/biom12111651
Chicago/Turabian StyleMorea, Veronica, Francesco Angelucci, Jeremy R. H. Tame, Enrico Di Cera, and Andrea Bellelli. 2022. "Structural Basis of Sequential and Concerted Cooperativity" Biomolecules 12, no. 11: 1651. https://doi.org/10.3390/biom12111651