Using surface plasmon resonance to directly determine binding affinities of combinatorially selected cyclopeptides and their linear analogs to a streptavidin chip

Chang, Yi‐Pin; Chu, Yen‐Ho

doi:10.1016/j.ab.2005.01.020

Cited by 20 publications

(12 citation statements)

References 29 publications

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“…The propensity of the eight octapeptides to assume secondary structures correlated with their inhibitory activities. Previous studies have shown entropy-mediated gains in affinity by constraining the conformational freedom of ligands (37)(38)(39)(40)(41)(42). In the present study, spontaneous prestructuring of the peptide might reduce the entropic penalty associated with formation of a peptide/hTS complex.…”

Section: Resultsmentioning

confidence: 58%

Protein–protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Cardinale

Guaitoli

Tondi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

157

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The undersigned authors note the following: "We wish to bring to your attention an issue regarding our PNAS publication referenced above. Although we cite our earlier PNAS publication (see ref. Figs. 2 and 3 display the UWHBs for Hb β-subunit (pdb.1bz0, chain B) and human cellular prion protein (pdb.1qm0) (12)(13)(14). Within the natural interactive context of the Hb subunit, the UWHBs signal crucial binding regions (24): UWHBs (90, 94), (90, 95) are associated with the β-FG corner involved in the quaternary α1β2 interface; UWHB (5, 9) is adjacent to Glu-6 which in sickle cell anemia mutates to Val-6 and is located at the Val-6-(Phe-85, Leu-88) interface in the deoxyHbS fiber."The following text in the section titled 'Toward a Structural Diagnosis' on page 6449 of our text is similar to the text beginning in the last paragraph on page 2392 in ref. 23:The distribution of proteins according to their average extent of hydrogen bond wrapping and their spatial concentration of structural defects is shown in Fig. 5 (see also ref. 23). The sample of 2,811 PDB proteins is large enough to define a reliable abundance distribution with an inflection point at ρ = 6.20. The integration of the distribution over a ρ-interval gives the fraction of proteins whose ρ lies within that range. Of the 2,811 proteins examined, 2,572 have ρ > 6.20, and none of them is known to yield amyloid aggregation under physiological conditions entailing partial retention of structure. Strikingly, relatively few disease-related amyloidogenic proteins are known in the sparsely populated, underwrapped 3.5 < ρ < 6.20 range, with the cellular prion proteins located at the extreme of the spectrum (3.53 < ρ < 3.72)....The range of H-bond wrapping 3.5 < ρ < 4.6 of 20 sampled PDB membrane proteins has been included in Fig. 5 for comparison. As expected, such proteins do not have the stringent H-bond packing requirements of soluble proteins for their H bonds at the lipid interface. Thus, this comparison becomes suggestive in terms of elucidating the driving factor for aggregation in soluble proteins: Although the UWHB constitutes a structural defect in a soluble protein because of its vulnerability to water attack, it is not a structural defect in a membrane protein. The exposure of the polar amide and carbonyl of the unbound state to a nonpolar phase is thermodynamically unfavorable (22). The virtually identical ρ value for human prion and outer-membrane protein A (Fig. 5) is revealing in this regard.Furthermore, all known amyloidogenic proteins that occur naturally in complexed form have sufficient H-bond wrapping within their respective complexes (ρ value near 6.2). Their amyloidogenic propensity appears only under conditions in which the protein is dissociated from the complex (compare Fig. 5). This finding is corroborated by the following computation. If an intramolecular hydrogen bond is underwrapped within the isolated protein molecule but located at an interface upon complexation, then to determine its extent of wrapping within the complex, we take ...

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Section: Resultsmentioning

confidence: 58%

Protein–protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Cardinale

Guaitoli

Tondi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

157

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“…Chang and co-worker observed that linear peptides are low-affinity ligands, which do not have a distinct conformation in solution. The corresponding cyclic peptides bound 1000-fold firmer than their linear counterpart [34], because the peptides were constrained by cyclisation and lose their conformational freedom. Correspondingly, the entropy of such unbound peptides is reduced [34,35].…”

Section: Resultsmentioning

confidence: 99%

“…The corresponding cyclic peptides bound 1000-fold firmer than their linear counterpart [34], because the peptides were constrained by cyclisation and lose their conformational freedom. Correspondingly, the entropy of such unbound peptides is reduced [34,35]. This entropy decrease is also achieved by an arrangement into a micelle.…”

Section: Resultsmentioning

confidence: 99%

Self-assembled peptide amphiphiles function as multivalent binder with increased hemagglutinin affinity

et al. 2013

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BackgroundA promising way in diagnostic and therapeutic applications is the development of peptide amphiphiles (PAs). Peptides with a palmitic acid alkylchain were designed and characterized to study the effect of the structure modifications on self-assembling capabilities and the multiple binding capacity to hemagglutinin (HA), the surface protein of influenza virus type A. The peptide amphiphiles consists of a hydrophilic headgroup with a biological functionality of the peptide sequence and a chemically conjugated hydrophobic tail. In solution they self-assemble easily to micelles with a hydrophobic core surrounded by a closely packed peptide-shell.ResultsIn this study the effect of a multiple peptide binding partner to the receptor binding site of HA could be determined with surface plasmon resonance measurements. The applied modification of the peptides causes signal amplification in relationship to the unmodified peptide wherein the high constant specificity persists. The molecular assembly of the peptides was characterized by the determination of critical micelle concentration (CMC) with concentration of 10-5 M and the colloidal size distribution.ConclusionThe modification of the physico-chemical parameters by producing peptide amphiphiles form monomeric structures which enhances the binding affinity and allows a better examination of the interaction with the virus surface protein hemagglutinin.

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“…[33][34][35][36][37] Since then, a handful of studies have appeared in which constrained systems have been examined in a controlled fashion, and which have taken advantage of the availability of calorimetric methods to measure the underlying thermodynamic binding parameters; these have included carbohydrates 38,39 as well as peptides [40][41][42][43] and peptidomimetic scaffolds. [44][45][46] FIGURE 1 Theoretical behavior of conformational entropy in the case of a flexible ligand and corresponding constrained analog.…”

Section: Conformational Constraint In Protein Ligand Design and The Imentioning

confidence: 99%

Conformational constraint in protein ligand design and the inconsistency of binding entropy

Udugamasooriya

Spaller

2008

Biopolymers

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It is an accepted practice in ligand design to introduce conformational constraint with the expectation of improving affinity, justified by the theoretical possibility that an unfavorable change in binding entropy will be reduced. This rationale of minimizing the entropic penalty through imposing structural constraints upon a ligand, however, has been voiced more often than verified. Here we examine three modified cyclic peptides, along with multiple versions of their linear control analogs, and determine their thermodynamic parameters when binding the same host, the third PDZ domain (PDZ3) of the mammalian postsynaptic density-95 (PSD-95) protein. To begin a two-stage investigation, the initial evaluation involved solution binding studies with isothermal titration calorimetry (ITC), which provided the changes in Gibbs free energy (DeltaG), enthalpy (DeltaH), and entropy (TDeltaS) upon formation of the protein-ligand complex. In the second stage, a selected macrocycle along with two matched linear controls were subjected to more rigorous analysis by ITC, which included (1) change in heat of buffer ionization (DeltaH(ion)) titrations, to examine the role of proton transfer events; (2) change in heat capacity (DeltaC(p)) determinations, to indirectly probe the nature of the binding surface; and (3) osmotic stress experiments, to evaluate desolvation effects and quantitate water release. Together, these demonstrate that the entropic relationship between a macrocyclic ligand and a linear counterpart can be a complex one that is difficult to rationalize. Further, the addition of constraint can, counterintuitively, lead to a less favorable change in binding entropy. This underscores the need to use matched linear control ligands to assure that comparisons are made in a meaningful manner.

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Using surface plasmon resonance to directly determine binding affinities of combinatorially selected cyclopeptides and their linear analogs to a streptavidin chip

Cited by 20 publications

References 29 publications

Protein–protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Protein–protein interface-binding peptides inhibit the cancer therapy target human thymidylate synthase

Self-assembled peptide amphiphiles function as multivalent binder with increased hemagglutinin affinity

Conformational constraint in protein ligand design and the inconsistency of binding entropy

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