An immunological approach to the conformational equilibrium of staphylococcal nuclease.

The conformational equilibrium constant, K_conf, of staphylococcal nuclease, describing the equilibrium between the native conformation and non-native or disordered conformations, has been estimated using an immunologic method and an interpretive model. Using goat antisera prepared toward a conformationally disordered nuclease fragment (99–149), antibodies specific for the disordered form of the helix-rich sequence 99 to 126, anti-(99–126)_R, were isolated by sequential immunoabsorption. Anti-(99–126)_R forms soluble 7 S complexes with fragment (99–149), but this interaction may be inhibited by a large excess of nuclease. By using fragment (99–149) preferentially carbamylated at the α-amino terminus with KN¹⁴CO and rabbit anti-goat immunoglobulin to distinguish between antibody-bound and free fragment (99–149), an assay for the quantitation of the degree of inhibition of anti-(99–126)_R. (99–149) complex formation by nuclease was developed.Using a formal analysis based on the hypothesis that nuclease is in a conformational equilibrium between a folded and unfolded form and that anti-(99–126)_R binds effectively only to the unfolded form, the K_conf of nuclease was estimated to be 2900. In the presence of the ligands Ca(II), or Ca(II) and thymidine-3′,5′-diphosphate, K_conf values of 6500 and 30,000 to 50,000 were estimated, respectively. The K_conf of nuclease at 4 °C and 39 °C was 3900 and 400, respectively.     

FKBP-like catalysis of peptidyl-prolyl bond isomerization by micelles and membranes

Under physiological conditions, peptidyl-prolyl cis/trans isomerases catalyze powerfully the cis/trans isomerization of the -Xaa-Pro- bond (Xaa: natural amino acids) in oligopeptides and proteins (PPIases; EC 5.2.1.8). However, incorporation of proline containing tetrapeptide-4-nitroanilides in micelles and phospholipid vesicles also leads to increased rates of this unimolecular conformational interconversion. The isomerization rate was dependent on the detergent and vesicle concentration, respectively. The observed rate constants fit the pseudophase model of micellar catalysis allowing the calculation of micellar turnover numbers (k_cis^mic) and dissociation constants (K_C^mic). Comparing k_cis^mic values to the rate constants of the uncatalyzed cis to trans isomerization, an acceleration factor of about 20-fold was obtained for Suc-Ala-Phe-Pro-Phe-4-nitroanilide (Suc: succinyl) bound to zwitterionic SB12 (N-dodecyl-N,N-dimethylammonium-3-propanesulfonate) micelles. In addition, a marked increase in the population of the trans conformer relative to cis was noted for all investigated combinations of peptides and detergents. In a series of tetrapeptides, Suc-Ala-Xaa-Pro-Phe-4-nitroanilide k_cis^mic/K_C^mic as well as k_cis^mic values are linearly correlated with the high performance liquid chromatography capacity factor R′ describing the hydrophobicity of the amino acid Xaa. The same correlation can describe quantitatively the dependency of k_car/K_m on substrate hydrophobicity for the FKBP12-catalyzed isomerization. Despite the great differences in catalytic power, these results confirm the suspicion that micelles and FKBP12 may share a common component in the catalytic mechanism of peptidyl-prolyl bond isomerization. © 1997 John Wiley & Sons, Inc. Biopoly 42: 49–60, 1997     

Studies of the mechanism of action and regulation of cAMP-dependent protein kinase

Magnetic resonance and kinetic studies of the catalytic subunit of a Type II cAMP-dependent protein kinase from bovine heart have established the active complex to be an enzyme-ATP-metal bridge. The metal ion is β,γ coordinated with Δ chirality at the β-phosphorous atom. The binding of a second metal ion at the active site which bridges the enzyme to the three phosphoryl groups of ATP, partially inhibits the reaction. Binding of the metal-ATP substrate to the enzyme occurs in a diffusion-controlled reaction followed by a 40 ° change in the glycosidic torsional angle. This conformational change results from strong interaction of the nucleotide base with the enzyme. NMR studies of four ATP-utilizing enzymes show a correlation between such conformational changes and high nucleotide base specificity. Heptapeptide substrates and substrate analogs bind to the active site of the catalytic subunit at a rate significantly lower than collision frequency indicating conformational selection by the enzyme or a subsequent slow conformational change. NMR studies of the conformation of the enzyme-bound peptide substrates have ruled out α-helical and β-pleated sheet structures. The results of kinetic studies of peptide substrates in which the amino acid sequence was systematically varied were used to rule out the obligatory requirement for all possible β-turn conformations within the heptapeptide although an enzymatic preference for a β_2–5 or β_3–6 turn could not be excluded. Hence if protein kinase has an absolute requirement for a specific secondary structure, then this structure must be a coil. In the enzyme-substrate complex the distance along the reaction coordinate between the γ-P of ATP and the serine oxygen of the peptide substrate (5.3 ± 0.7 Å) allows room for a metaphosphate intermediate. This finding together with kinetic observations as well as the location of the inhibitory metal suggest a dissociative mechanism for protein kinase, although a mechanism with some associative character remains possible. Regulation of protein kinase is accomplished by competition between the regulatory subunit and peptide or protein substrates at the active site of the catalytic subunit. Thus, the regulatory subunit is found by NMR to block the binding of the peptide substrate to the active site of protein kinase but allows the binding of the nucleotide substrate and divalent cations. The dissociation constant of the regulatory subunit from the active site (10^?10m) is increased ~10-fold by phosphorylation and ~10⁴-fold by the binding of cAMP, to a value (10^?5m) which exceeds the intracellular concentration of the R₂C₂ holoenzyme complex (10^?6m). The resulting dissociation of the holoenzyme releases the catalytic subunit, permitting the active site binding of peptide or protein substrates.     

Dissociation of pig liver carboxylesterase measured by quantitative micro-complement fixation

Rate and apparent equilibrium constants for the dissociation of pig liver carboxylesterase into three subunit molecules have been determined by complement fixation. The dependence of the dissociation equilibria on pH are consistent with dissociation reactions involving the addition of two protons per subunit, a pH-independent dissociation, and a dissociation upon the loss of one proton per subunit. The rate constants for dissociation are consistent with terms first order in hydrogen and hydroxide ions and a pH-independent path. The equilibrium constants in the range 3–35 °C at pH 7.2 exhibit no dependence on temperature; the association reaction is entropy driven with $\text{ΔS = 68}\text{cal mol}{}^{\mathrm{?1}}{}^{\mathrm{°}}\text{K}{}^{\mathrm{?1}}$. The rate constants for the pH-independent dissociation follow ΔH^≠ ? 6 kcal mol^?1. The order of effectiveness of concentrated salts in promoting denaturation is correlated with their effect on the activity coefficient of acetyltetraglycine ethyl ester and suggests that peptide groups become more exposed upon dissociation. The increased dissociation in the presence of urea derivatives containing alkyl substituents suggests exposure of hydrophobic regions upon dissociation; this is also consistent with ΔH = 0 for dissociation. It is likely that hydrophobic interactions contribute to the stability of the trimeric whole molecule.     

Implications of the Alternating Access Model for Organic Anion Transporter Kinetics

Many transport proteins, including the clinically important organic anion transporters (OATs), appear to function via an “alternating access” mechanism. In analyzing the kinetics of these transporters, the terms K _m and V _max are often treated in the field as denoting, respectively, the affinity of the substrate for the transporter and the turnover (conformational switch) rate of the substrate–transporter complex. In fact, the expressions for both these parameters have very complex forms comprising multiple rate constants from conformational switch as well as association/dissociation steps in the cycling of the transporter and, therefore, do not have straightforward physical meanings. However, if the rapid equilibrium assumption is made (namely, that the association/dissociation steps occur far more rapidly than the conformational switch steps), these expressions become greatly simplified and their physical meaning clear, though still distinct from the conventional interpretations. V _max will be a function of not just the rate of substrate–transporter complex turnover but also the rate of the “return” conformational switch and will vary largely with the slower of these two steps (the rate-limiting step). K _m will be seen to be related to substrate affinity by a term that varies inversely with the substrate–transporter complex turnover rate, essentially because the greater this rate, the greater the extent to which transporters will be distributed in a conformation inaccessible to substrate. Here, an intuitive approach is presented to demonstrate these conclusions. The phenomena of trans-stimulation and trans-inhibition are discussed in the context of this analysis.     

Nitrilotris(methylenephosphonates) in aqueous solution and solid state - dilatometric, potentiometric and NMR investigations

Dissociation and alkali complex formation equilibria of nitrilotris(methylenephosphonic acid) (NTMP, H₆L) have been studied by dilatometric, potentiometric and ³¹P NMR-controlled titrations. Dilatometry indicated the formation of alkali complexes ML (M=Li, Na, K, Rb, Cs) at high pH with a stability decreasing from Li to Cs. An efficient combination of potentiometric and NMR methods confirmed two types of alkali metal complexes MHL and ML. Stability constants for the equilibria following M⁺ + HL⁵⁻ ? MHL⁴⁻ and M⁺ + L⁶⁻ ? ML⁵⁻, respectively, were determined: logK_NaHL=1.08(0.07), logK_KHL=0.86(0.08), logK_NaL=2.24(0.03). Systematic errors are introduced by using alkali metal hydroxides as titrants for routine potentiometric determinations of dissociation constants pK_a5^app and pK_a6^app. Correction formulae were derived to convert actual dissociation constants pK_a into apparent dissociation constants pK_a^app (or vice versa). The actual dissociation constants were found: pK_a5(H₂L⁴⁻ ? H⁺ + HL⁵⁻)=7.47(0.03) and pK_a6(HL⁵⁻ ? H⁺ + L⁶⁻)=14.1(0.1). The anisotropy of ³¹P chemical shifts of salts M_nH_6 − nL (M=Li, Na, n=0-5) is more sensitive towards titration (n) than isotropic solution state chemical shifts.     

The First and Second Dissociation Constants of Subtilisin BPN′-Plasminostreptin Complex Determined by a Polarographic Method,and the Effects of pH on Them

A polarographic method based on the Brdi?ka current (the polarographic catalytic hydrogen evolution current produced by proteins in the presence of cobalt salts) was applied to direct titration of subtilisin BPN′ (S.BPIST) with plasminostreptin (PS) at a concentration level of 10”⁸ m. The first and second dissociation constants of the S.BPN-PS complex were determined by fitting theoretical curves to the titration data, in which the multiple equilibria involving microscopically distinct forms of S.BPN-PS complex were taken into account. The intrinsic free energy change in the first binding of S.BPN′ to dimeric PS was larger than that in the second binding. The dependence of the microscopic dissociation constants of S.BPN′-PS complex on pH indicates the participation of ionizable groups of pK_a 8.0 and 9.4 in the complex formation. The repulsive effect between negatively charged molecules of S.BPN′ and PS in the complex formation at elevated pH is suggested.     

Kinetic Mechanisms of Fast Glutamate Sensing by Fluorescent Protein Probes

We have developed probes based on the bacterial periplasmic glutamate/aspartate binding protein with either an endogenously fluorescent protein or a synthetic fluorophore as the indicator of glutamate binding for studying the kinetic mechanism of glutamate binding. iGluSnFR variants termed iGlu_h, iGlu_m, and iGlu_l cover a broad range of K_d-s (5.8 μM and 2.1 and 50 mM, respectively), and a novel fluorescently labeled indicator, Fl-GluBP, has a K_d of 9.7 μM. The fluorescence response kinetics of all the probes are consistent with a two-step mechanism involving ligand binding and isomerization either of the apo or the ligand-bound binding protein. Although the previously characterized ultrafast indicators iGlu_u and iGlu_f had monophasic fluorescence enhancement that occurred in the rate limiting isomerization step, the sensors described here all have biphasic binding kinetics with fluorescence increases occurring both in the glutamate binding and the isomerization steps. For iGlu_m and iGlu_l, the data indicate prebinding conformational change followed by ligand binding. In contrast, for iGlu_h and Fl-GluBP, glutamate binding is followed by isomerization. Thus, the effects of structural heterogeneity introduced by single amino acid changes around the binding site on the kinetic path of interactions with glutamate are revealed. Remarkably, glutamate binding with a diffusion-limited rate constant to iGlu_h and Fl-GluBP is detected for the first time, hinting at the underlying mechanism of the supremely rapid activation of the highly homologous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor by glutamate binding.     

Poly-acid properties of biosynthetic hyaluronan studied by titration

In this study the poly-acid properties of biosynthetic hyaluronan produced by fermentation of Bacillus subtilis have been investigated. Potentiometric titration as well as ¹H NMR titration have been used to determine the dissociation constants of the carboxylic group on hyaluronic acid. The intrinsic pK_a and pK_{a, α=0.5} were determined in the presence of 0.1 M salt to be 2.99 and 3.37, respectively. The pK_{a, α=0.5} was found to be unaffected by variations in the ionic strength which is in good agreement with the fact that at α = 0.5, 50% of the carboxylic moieties on the hyaluronan are charged. On the other hand the intrinsic pK_a was found to be dependent on the ionic strength until the Debye-Hückel screening length approaches the length of repeating disaccharide unit of hyaluronic acid.Our findings are in good agreement with previously determined dissociation constants for other sources of hyaluronan. We have also shown that ¹H NMR spectroscopy is the preferred method for polyelectrolyte titration because of the ability to isolate the contribution of several ionisable groups on a polymer on molecular level.     

Kinetics of interaction of some α- and β-D-monosaccharides with concanavalin A

The rates of formation and dissociation of concanavalin A with some 4-methylumbelliferyl and p-nitrophenyl derivatives of α- and β-D-mannopyranosides and glucopyranosides were measured by fluorescence and spectral stopped-flow methods. All process examined were uniphasic. The second-order formation rate constants varied only from 6.8 · 10⁴ to 12.8 · 10⁴ M^?. s^?1, whereas the first-order dissociation rate constants ranged from 4.1. to 220 s^?1, all at ph 5.0, I = 0.3 M, and 25°C. Dissociation rates thus controlled the value of binding constant. The effect of temperature on these reactions was examined, from which enthalpies and entropies of activation and of reaction could be calculated. The effects of pH at 25°C on the reaction rates of 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside with concanavalin A were examined. The value of the binding constant K_ap (derived from the kinetics) at any pH could be related to the intrinsic binding constant K by the expression K_ap = K_aK(K_a + [H⁺])^?1. The values of K_a, the ionization constant of the protein segment responsive to sugar binding, were 3 · 10^?4 M and 1 · 10^?4 M for 4-methylumbelliferyl α-D-mannopyranoside and 4-methylumbelliferyl α-D-glucopyranoside, respectively. The binding constant of p-nitrophenyl α-D-mannopyranoside is surprisingly much less sensitive to a pH change from 5.0 to 2.7. Ionic strength had little effect on the binding characteristics of 4-methylumbelliferyl α-D-mannopyranoside to concanavalin A at pH 5.2 and 25°C.     

Reactions of the amino groups in ribonuclease A: I. Kinetic studies

A kinetic analysis has been made of the reaction of the amino groups of ribonuclease A with trinitrobenzene-sulfonic acid. The number of reactive groups and the number of subsets were markedly dependent on the nature and concentrations of the buffer and the pH. Apparent values of pK_a, calculated from the variation of the velocity constants with pH, could, in general, be obtained only for pH values above 7.4. Below this pH the velocity constants were greater than the values calculated from the intrinsic constants. The values of pK_a were in the range of 7.9 – 9.0, which are somewhat smaller than those derived from titration data.The change of behavior of the amino groups with pH is confirmed by a study of the effects of ionic strength on the reactions.The velocity constants generally appear to decrease with increasing concentration of protein.It is shown that there is a close correlation between the pH region in which large changes occur of the reactivities of the amino groups of RNase and the kinetics of the enzyme reaction.     

Structure of [NiFe] hydrogenase maturation protein HypE from Escherichia coli and its interaction with HypF

Hydrogenases are enzymes involved in hydrogen metabolism, utilizing H₂ as an electron source. [NiFe] hydrogenases are heterodimeric Fe-S proteins, with a large subunit containing the reaction center involving Fe and Ni metal ions and a small subunit containing one or more Fe-S clusters. Maturation of the [NiFe] hydrogenase involves assembly of nonproteinaceous ligands on the large subunit by accessory proteins encoded by the hyp operon. HypE is an essential accessory protein and participates in the synthesis of two cyano groups found in the large subunit. We report the crystal structure of Escherichia coli HypE at 2.0-Å resolution. HypE exhibits a fold similar to that of PurM and ThiL and forms dimers. The C-terminal catalytically essential Cys336 is internalized at the dimer interface between the N- and C-terminal domains. A mechanism for dehydration of the thiocarbamate to the thiocyanate is proposed, involving Asp83 and Glu272. The interactions of HypE and HypF were characterized in detail by surface plasmon resonance and isothermal titration calorimetry, revealing a K_d (dissociation constant) of ~400 nM. The stoichiometry and molecular weights of the complex were verified by size exclusion chromatography and gel scanning densitometry. These experiments reveal that HypE and HypF associate to form a stoichiometric, hetero-oligomeric complex predominantly consisting of a [EF]₂ heterotetramer which exists in a dynamic equilibrium with the EF heterodimer. The surface plasmon resonance results indicate that a conformational change occurs upon heterodimerization which facilitates formation of a productive complex as part of the carbamate transfer reaction.     

Evolution of Metamorphism in Thymidylate Synthases Within the Primate Lineages

Crystal structures of human thymidylate synthase (hTS) revealed that the protein exists in active and inactive conformations, defined by the position of a loop containing the active site nucleophile. TS is highly homologous among diverse species; however, the residue at position 163 (hTS) differs among species. Arginine at this position is predicted by structural modeling to enable conformational switching. Arginine or lysine is reported at this position in all mammals in the GenBank and Ensembl databases, with arginine reported in only primates. Sequence analysis of the TS gene of representative primates revealed that arginine occurs at this relative position in all primates except a representative of prosimians. Mutant human proteins were created with residues at position 163 that occur in TSs from prokaryotes and eukaryotes. Catalytic constants (k _cat) of mutant enzymes were 45–149% of hTS, with the lysine mutant (R163K) exhibiting the highest k _cat. The effect of lysine substitution on solution structure and on ligand binding was investigated. R163K exhibited higher intrinsic fluorescence, a more negative molar ellipticity, and higher dissociation constants (K _d) for ligands that modulate protein conformation than hTS. Temperature effects on intrinsic fluorescence and catalytic activity of hTS and R163K are consistent with proteins populating different conformational states. The data indicate that the enzyme with arginine at the position corresponding to 163 (hTS) evolved after the divergence of prosimians and simians and that substitution of lysine by arginine confers unique structural and functional properties to the enzyme expressed in simian primates.     

Temperature dependence of acetylcholine receptor channels activated by different agonists

The temperature dependence of agonist binding and channel gating were measured for wild-type adult neuromuscular acetylcholine receptors activated by acetylcholine, carbamylcholine, or choline. With acetylcholine, temperature changed the gating rate constants (Q₁₀ ≈ 3.2) but had almost no effect on the equilibrium constant. The enthalpy change associated with gating was agonist-dependent, but for all three ligands it was approximately equal to the corresponding free-energy change. The equilibrium dissociation constant of the resting conformation (K_d), the slope of the rate-equilibrium free-energy relationship (Φ), and the acetylcholine association and dissociation rate constants were approximately temperature-independent. In the mutant αG153S, the choline association and dissociation rate constants were temperature-dependent (Q₁₀ ≈ 7.4) but K_d was not. By combining two independent mutations, we were able to compensate for the catalytic effect of temperature on the decay time constant of a synaptic current. At mouse body temperature, the channel-opening and -closing rate constants are ∼400 and 16 ms⁻¹. We hypothesize that the agonist dependence of the gating enthalpy change is associated with differences in ligand binding, specifically to the open-channel conformation of the protein.     

Genetic noise control via protein oligomerization

Background

Biochemical equilibria are usually modeled iteratively: given one or a few fitted models, if there is a lack of fit or over fitting, a new model with additional or fewer parameters is then fitted, and the process is repeated. The problem with this approach is that different analysts can propose and select different models and thus extract different binding parameter estimates from the same data. An alternative is to first generate a comprehensive standardized list of plausible models, and to then fit them exhaustively, or semi-exhaustively.

Results

A framework is presented in which equilibriums are modeled as pairs (g, h) where g = 0 maps total reactant concentrations (system inputs) into free reactant concentrations (system states) which h then maps into expected values of measurements (system outputs). By letting dissociation constants K _d be either freely estimated, infinity, zero, or equal to other K _d , and by letting undamaged protein fractions be either freely estimated or 1, many g models are formed. A standard space of g models for ligand-induced protein dimerization equilibria is given. Coupled to an h model, the resulting (g, h) were fitted to dTTP induced R1 dimerization data (R1 is the large subunit of ribonucleotide reductase). Models with the fewest parameters were fitted first. Thereafter, upon fitting a batch, the next batch of models (with one more parameter) was fitted only if the current batch yielded a model that was better (based on the Akaike Information Criterion) than the best model in the previous batch (with one less parameter). Within batches models were fitted in parallel. This semi-exhaustive approach yielded the same best models as an exhaustive model space fit, but in approximately one-fifth the time.

Conclusion

Comprehensive model space based biochemical equilibrium model selection methods are realizable. Their significance to systems biology as mappings of data into mathematical models warrants their development.     

Mixed and uniform co-operativity of ligand binding to multisite proteins: the co-operativity types allowed by the adair equation and conditions for them

It is proved for the first time that the macroscopic co-operativity of binding to a protein with q binding sites may change signs over a single binding curve any number of times from 0 to (q-2), but no more than (q-2). n changes of sign of macroscopic co-operativity requires as a necessary condition at least n changes of sign of microscopic co-operativity, but this necessary condition is not a sufficient one. The necessary and sufficient condition that decides whether there are two changes of sign in a four-site protein is obtained. There are no changes when K₁K₃(K₂-K₄)+K₁K₂(K₃-K₂)+K₂K₃(K₄-K₃) is positive, and two changes when it is negative, presuming the above mentioned necessary conditions to be satisfied. The K's of this formula are the “intrinsic” per-site Adair constants. As a result, the conditions for all six co-operativity types possible with a four-site protein are now known.     

Oxyhemoglobin dissociation curve as expo-exponential paradigm of asymmetric sigmoid function.

From the assumption that the fractional increase of HbO₂ as a function of pO₂ is proportional to HbO₂, and that the proportionality coefficient of that relation decreases exponentially with pO₂, an equation can be derived that gives an excellent fit to the full range of the oxyhemoglobin dissociation curve. To generate this asymmetric sigmoid curve, only one rate constant is required. In addition, the initial and final conditions specify an intermediate constant B, the “shift factor” that determines the horizontal displacement of the curve. The rate constant K specifies the rate of change of the specific rate of increase of HbO₂ with respect to O₂. Governing the slope of the curve, K decreases as temperature and acidity increase, while the B factor remains constant. For Hb in solution, B decreases with decrease of concentration, but K appears to be unchanged. The expo-exponential constants provide convenient specification of the full course and position of the oxyhemoglobin dissociation curve.     

Structural origins of high apparent dielectric constants experienced by ionizable groups in the hydrophobic core of a protein

The side chains of Lys66, Asp66, and Glu66 in staphylococcal nuclease are fully buried and surrounded mainly by hydrophobic matter, except for internal water molecules associated with carboxylic oxygen atoms. These ionizable side chains titrate with pK_a values of 5.7, 8.8, and 8.9, respectively. To reproduce these pK_a values with continuum electrostatics calculations, we treated the protein with high dielectric constants. We have examined the structural origins of these high apparent dielectric constants by using NMR spectroscopy to characterize the structural response to the ionization of these internal side chains. Substitution of Val66 with Lys66 and Asp66 led to increased conformational fluctuations of the microenvironments surrounding these groups, even under pH conditions where Lys66 and Asp66 are neutral. When Lys66, Asp66, and Glu66 are charged, the proteins remain almost fully folded, but resonances for a few backbone amides adjacent to the internal ionizable residues are broadened. This suggests that the ionization of the internal groups promotes a local increase in dynamics on the intermediate timescale, consistent with either partial unfolding or increased backbone fluctuations of helix 1 near residue 66, or, less likely, with increased fluctuations of the charged side chains at position 66. These experiments confirm that the high apparent dielectric constants reported by internal Lys66, Asp66, and Glu66 reflect localized changes in conformational fluctuations without incurring detectable global structural reorganization. To improve structure-based pK_a calculations in proteins, we will need to learn how to treat this coupling between ionization of internal groups and local changes in conformational fluctuations explicitly.     

Peptide Scaffold-Based Discovery of Nonpeptide Natural Medicines to Target PI3K p85 SH2 Domain

Targeting phosphoinositide 3-kinase (PI3K) has been recognized as an attractive strategy for anticancer therapy. The PI3K is a heterodimer composed of a catalytic subunit p110 and a regulatory subunit p85. Here, instead of targeting the catalytic p110 that has been considered previously, we purposed targeting the peptide-recognition domain SH2 of regulatory p85 with natural medicines obtained by using a peptide scaffold-based screening scheme. In the procedure, a core binding motif was extracted from the cocrystallized complex of a cognate phosphopeptide with the domain, which was considered as basic scaffold to perform high-through virtual screening against a structurally diverse, nonredundant library of natural products. A number of hit compounds with high binding potency to the domain and significant conformational similarity with the peptide scaffold were identified; in vitro affinity assay confirmed that five hits have moderate or high affinity for the domain with measured dissociation constants K_d range between 25 and 360 μM, which are comparable to or even better than that of the cognate phosphopeptide SDpYMNMTP and its core motif peptide pYMNM (K_d?=?15 and 32 μM, respectively). Structural analysis and nonbonded comparison of SH2 interactions with phosphopeptides and potent hit compounds revealed that only negatively charged phosphate and, sometime, sulfate can confer domain-binding capability to small-molecule compounds, but carboxylate cannot. A similar binding mode of compounds with phosphopeptide is important for the compounds to have high affinity and specificity.