Cooperative kinetics of ligand binding to linear polymers

Measurements of light scattering have given much information about formation and properties of fibrin. These studies have determined mass-length ratio of linear polymers (protofibrils) and of fibers, kinetics of polymerization and of lateral association and volume-mass ratio of thick fibers. This ratio is 5 to 1. On the one hand, this high value suggests that the fiber contains channels that allow the diffusion of enzymes such as Factor XHIa and plasmin; on the other hand, the high value appears paradoxical for a stiff fiber made up of elongated units (fibrin monomers) arranged in parallel. Such a high fiber volume is a property of only a small set out of many high-symmetry models of fibrin, which may be constructed from overlapping three-domain monomers which are arranged into strands, are aligned nearly parallel to the fiber axis and make adequate longitudinal and lateral contacts. These models contain helical protofibrils related to each other by rotation axes parallel to the fiber axis. The protofibrils may contain 2, 3 or 4 monomers per helical turn and there are four possible symmetries. A large specific volume is achieved if the ends of each monomer are slightly displaced from the protofibril axis, either by a shift or by a tilt of the monomer. The fiber containing tilted monomers is more highly interconnected; the two ends of a tilted monomer form lateral contacts with different adjacent protofibrils, whereas the two ends of a non-tilted monomer contact the same adjacent protofibril(s).

Faculty Opinions recommendation of The kinetics of ligand binding by an adenine-sensing riboswitch.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1028329.334943 ◽

2005 ◽

Author(s):

Scott Silverman

Keyword(s):

Ligand Binding ◽

The Kinetics of Ligand Binding and of the Association-Dissociation Reactions of Human Hemoglobin

10.1016/s0021-9258(18)62253-7 ◽

1971 ◽

Vol 246 (9) ◽

pp. 2796-2807 ◽

Cited By ~ 21

Author(s):

Melvin E. Andersen ◽

J. Keith Moffat ◽

Quentin H. Gibson

Keyword(s):

Ligand Binding ◽

Human Hemoglobin ◽

Electrostatic influence on the kinetics of ligand binding to acetylcholinesterase. Distinctions between active center ligands and fasciculin.

10.1016/s0021-9258(19)89415-2 ◽

1998 ◽

Vol 273 (19) ◽

pp. 11986

Author(s):

Zoran Radic ◽

Paul D. Kirchhoff ◽

Daniel M. Quinn ◽

J. Andrew McCammon ◽

Palmer Taylor

Keyword(s):

Ligand Binding ◽

Active Center ◽

Equilibria and Kinetics of Ligand Binding by Leghemoglobin from Soybean Root Nodules

10.1016/s0021-9258(19)45733-5 ◽

1972 ◽

Vol 247 (2) ◽

pp. 521-526

Author(s):

Takashi Imamura ◽

Austen Riggs ◽

Quentin H. Gibson

Keyword(s):

Ligand Binding ◽

Root Nodules ◽

Soybean Root ◽

Kinetics of ligand binding to Pseudoterranova decipiens and Ascaris suum hemoglobins and to Leu-29–>Tyr sperm whale myoglobin mutant

10.1016/s0021-9258(19)85292-4 ◽

1993 ◽

Vol 268 (23) ◽

pp. 16993-16998

Author(s):

Q.H. Gibson ◽

R. Regan ◽

J.S. Olson ◽

T.E. Carver ◽

B. Dixon ◽

...

Keyword(s):

Ligand Binding ◽

Ascaris Suum ◽

Sperm Whale ◽

Pseudoterranova Decipiens ◽

Kinetics Of ◽

Sperm Whale Myoglobin

Kinetics of large-ligand binding to one-dimensional lattices: theory of irreversible binding

Biopolymers ◽

10.1002/bip.1979.360180404 ◽

1979 ◽

Vol 18 (4) ◽

pp. 765-788 ◽

Cited By ~ 48

Author(s):

Irving R. Epstein

Keyword(s):

Ligand Binding ◽

Irreversible Binding ◽

One Dimensional ◽

Positive co-operative binding at two weak lysine-binding sites governs the Glu-plasminogen conformational change

Biochemical Journal ◽

10.1042/bj2850419 ◽

1992 ◽

Vol 285 (2) ◽

pp. 419-425 ◽

Cited By ~ 34

Author(s):

U Christensen ◽

L Mølgaard

Keyword(s):

Ligand Binding ◽

Binding Site ◽

Conformational Change ◽

Conformational Changes ◽

Binding Sites ◽

High Specificity ◽

Stopped Flow ◽

Protein Fluorescence ◽

Lysine Residues ◽

The kinetics of a series of Glu-plasminogen ligand-binding processes were investigated at pH 7.8 and 25 degrees C (in 0.1 M-NaCl). The ligands include compounds analogous to C-terminal lysine residues and to normal lysine residues. Changes of the Glu-plasminogen protein fluorescence were measured in a stopped-flow instrument as a function of time after rapid mixing of Glu-plasminogen and ligand at various concentrations. Large positive fluorescence changes (approximately 10%) accompany the ligand-induced conformational changes of Glu-plasminogen resulting from binding at weak lysine-binding sites. Detailed studies of the concentration-dependencies of the equilibrium signals and the rate constants of the process induced by various ligands showed the conformational change to involve two sites in a concerted positive co-operative process with three steps: (i) binding of a ligand at a very weak lysine-binding site that preferentially, but not exclusively, binds C-terminal-type lysine ligands, (ii) the rate-determining actual-conformational-change step and (iii) binding of one more lysine ligand at a second weak lysine-binding site that then binds the ligand more tightly. Further, totally independent initial small negative fluorescence changes (approximately 2-4%) corresponding to binding at the strong lysine-binding site of kringle 1 [Sottrup-Jensen, Claeys, Zajdel, Petersen & Magnusson (1978) Prog. Chem. Fibrinolysis Thrombolysis 3, 191-209] were observed for the C-terminal-type ligands. The finding that the conformational change in Glu-plasminogen involves two weak lysine-binding sites indicates that the effect cannot be assigned to any single kringle and that the problem of whether kringle 4 or kringle 5 is responsible for the process resolves itself. Probably kringle 4 and 5 are both participating. The involvement of two lysine binding-sites further makes the high specificity of Glu-plasminogen effectors more conceivable.