Binding ligands

Ligand binding and binding assay are dull, according to common prejudice, which is correct. Nevertheless, these simple assays often provide the key to interesting results. This is because the binding between two molecules is the first step in every biochemical reaction and thus every function. 

Many proteins do not have any ligands. No problem. You make one yourself. In epitope libraries you can find for every protein a host of peptides that bind to it with almost any affinity and at different sites (Scott and Smith 1990). The precondition is that the protein is pure and available in sufficient quantity. 

Enough of this pessimism. Binding projects are more predictable than others, and although the methods belong to the classics and thus provide little prestige they are nevertheless indispensable. 

it s my opinion the poor man should be content with what he can get, and not go looking for dainties in the bottom of the sea. 

In some cases, even a nontautomeric system can become a tautomeric species upon protonation if the molecule contains more than one protonable sites. The phenomenon of the tautomeric protonation was studied recently for 

The protonation at Nj (5) allows for the development of an O- H-Ni intramolecular hydrogen bond upon the formation of a five-member ring by the 0-CH2-CH2-N-H atoms. This structure stabilizes the O-CH2-CH2-N gauche arrangement, which would be favorably tram in the neutral form due to the repulsion of the O and N lone pairs. The formation of the O- H-N bond also modifies the relative position of the atom. In contrast, protonation at the 

N4 site (6) would basically maintain the O-CH2-CH2-N1 tram conformation. Furthermore, if the proton can stably reside at either site of the hgand molecule, the environment will dictate the site of the protonation, which could better support the ligand-protein interaction. 

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Wight C A and Armentrout P B 1993 Laser photoionization probes of ligand-binding effects in multiphoton dissociation of gas-phase transition-metal complexes ACS Symposium Series 530 61-74... 

Grubmiiller et al., 1996] Grubmiiller, H., Heymann, B., and Tavan, P. Ligand binding and molecular mechanics calculation of the streptavidin-biotin rupture force. Science. 271 (1996) 997-999... 

We have previously calculated conformational free energy differences for a well-suited model system, the catalytic subunit of cAMP-dependent protein kinase (cAPK), which is the best characterized member of the protein kinase family. It has been crystallized in three different conformations and our main focus was on how ligand binding shifts the equilibrium among these ([Helms and McCammon 1997]). As an example using state-of-the-art computational techniques, we summarize the main conclusions of this study and discuss a variety of methods that may be used to extend this study into the dynamic regime of protein domain motion. 

Helms and McCammon 1997] Helms, V., McCammon, J.A. Kinase Conformations A computational study of the effect of ligand binding. Prot. Sci. 6 (1997) 2336-2343... 

Both the AFM rupture experiments as well as our simulation studies focussed on the streptavidin-biotin complex as a model system for specific ligand binding. Streptavidin is a particularly well-studied protein and binds its ligand biotin with high affinity and specificity [51]. Whereas previous experiments (see references in Ref. [49]) and simulation studies [52] referred only to bound/unbound states and the associated kinetics, the recent AFM... 

Morton, A., Baase, W. A., Matthews, B. W. Energetic origins of specificity of ligand binding in an interior nonpolar cavity of T4 lysozyme. Biochemistry 34 (1995) 8564-8575. 

Flexible 3D alignment of a set of ligands binding to the same target and/or CoMFA analysis allowing the perception of a pharmacophore for this target. 

Depending on the information available about the protein structure and the ligands binding to a particular target, four different cases can be distinguished in drug design, as listed in Table 10.4-2. 

Hansson T, J Mturelius and J Aqvist 1998. Ligand Binding Affinity Prediction by Linear InteracHor Energy Methods. Journal of Computer-Aided Molecular Design 12 27-35. 

The equilibrium constant for a reaction in which a metal and a ligand bind to form a metal—ligand complex K ). 

Orstan, A. Wojcik, J. F. Spectroscopic Determination of Protein-Ligand Binding Constants, /. Chem. Educ. 1987, 64, 814-816. 

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