Synthesis and screening of libraries of synthetic tripodal receptor molecules with three different amino acid or peptide arms: identification of iron binders

A novel selectively deprotectable triazacyclophane scaffold was used for the design and split-mix synthesis of two libraries of solid-phase bound tripodal synthetic receptors possessing three different amino acid or peptidic arms. In the synthesis of the first library, the two outer arms consisted of amino acid Ala, Arg, Asp, Gln, Gly, Lys, Phe, Ser, Tyr, or Val and the middle arm consisted of amino acid Asn, Glu, His, Leu, or Pro. The second library contained amino acid and/or (di)peptide arms. The arms were different in all library members. The first outer arm consisted of amino acid(s) Ala, Arg, Gln, Phe, or Ser, the second outer arm consisted of amino acid(s) Asp, Gly, Lys, Tyr, or Val, and the middle arm consisted of amino acid(s) Asn, Glu, His, Leu, or Pro, leading to a 27 000 member library of synthetic tripodal receptor molecules. In on-bead screening experiments, a remarkable selectivity of some library members for Fe(3+) was observed and decoding of their structures by Edman degradation revealed consensus sequences with structural resemblance to non-heme iron proteins.     

Secondary Binding Interactions in a Synthetic Receptor for Trimethyllysine

We have systematically studied how secondary interactions with neighboring lysine (Lys) and arginine (Arg) residues influence the binding and selectivity of the synthetic receptor A₂N for trimethyllysine (Kme₃). Multiple secondary binding sites on A₂N are formed by carboxylates rigidly positioned over aromatic rings, a motif that has been shown to stabilize salt bridges. We varied the spacing between Kme_X (X=0, 3) and an ancillary Lys or Arg and measured binding by isothermal titration calorimetry (ITC). These studies revealed that both neighboring residues improve the binding of A₂N to Kme_X by approximately 1 kcal mol^?1, with little influence of the spacing. Nonetheless, the improvement in affinity caused by Arg is enthalpically driven, while for Lys it is entropically driven, suggesting different mechanisms by which the residues interact with the secondary binding site.     

An NMR Method To Pinpoint Supramolecular Ligand Binding to Basic Residues on Proteins

Targeting protein surfaces involved in protein–protein interactions by using supramolecular chemistry is a rapidly growing field. NMR spectroscopy is the method of choice to map ligand‐binding sites with single‐residue resolution by amide chemical shift perturbation and line broadening. However, large aromatic ligands affect NMR signals over a greater distance, and the binding site cannot be determined unambiguously by relying on backbone signals only. We herein employed Lys‐ and Arg‐specific H2(C)N NMR experiments to directly observe the side‐chain atoms in close contact with the ligand, for which the largest changes in the NMR signals are expected. The binding of Lys‐ and Arg‐specific supramolecular tweezers and a calixarene to two model proteins was studied. The H2(C)N spectra track the terminal CH₂ groups of all Lys and Arg residues, revealing significant differences in their binding kinetics and chemical shift perturbation, and can be used to clearly pinpoint the order of ligand binding.     

Small Cause,Great Impact: Modification of the Guanidine Group in the RGD Motif Controls Integrin Subtype Selectivity

Due to its unique role as a hydrogen‐bond donor and its positive charge, the guanidine group is an important pharmacophoric group and often used in synthetic ligands. The chemical modification of the guanidine group is often considered to destroy its function. Herein, we show that the N‐methylation, N‐alkylation, or N‐acylation of the guanidine group can be used to modify the receptor subtype specificity of the integrin ligand cilengitide. Using the αvβ6/α5β1‐biselective ligand c(isoDGRkphg) and the αvβ6‐specific ligand c(FRGDLAFp(NMe)K(Ac) as examples, we show that the binding affinities of the ligands can be fine‐tuned by this method to enhance the selectivity for αvβ6. Furthermore, we describe a new strategy for the functionalization of integrin ligands. By introducing longer N‐alkylguanidine and N‐acylguanidine groups, we are able to simultaneously identify a hitherto unknown anchoring point and enhance the subtype selectivity of the ligand.     

Application of an anhydrotrypsin-immobilized precolumn for selective separation of peptides having arginine or lysine at their C-termini by column-switching high-performance liquid chromatography

A column-switching high-performance liquid chromatographic (CS-HPLC) system which consisted of an anhydrotrypsin (AHT)-immobilized diol-silica precolumn and a reversed-phase analytical column was developed for the selective separation of peptides having Arg or Lys at their C-termini. Tuftsin (Thr-Lys-Pro-Arg) could be enriched almost quantitatively on the precolumn when loaded with water as a carrier solvent and the precolumn was washed with 10-30 mM acetate buffer (pH 5.0). An investigation of the affinity characteristics of 55 peptides to the AHT precolumn showed that among twelve peptides having Arg or ArgNH2 at their C-termini and more than four amino acid residues, ten were retained almost quantitatively on the precolumn, and eight out of nine peptides having Lys at their C-termini were less retained. The peptide having D-Arg at its C-termini was not retained. However, twelve out of thirty peptides having no Arg or Lys at their C-termini were also retained, but the retention was greatly decreased, in contrast to the Arg peptides, when the precolumn was washed with 20 mM calcium chloride solution. The results indicate that the CS-HPLC system equipped with an AHT precolumn offers new selectivity in the HPLC selectivity in the HPLC separation of peptides.     

Defining intrinsic hydrophobicity of amino acids' side chains in random coil conformation. Reversed-phase liquid chromatography of designed synthetic peptides vs. random peptide data sets

The two leading RP-HPLC approaches for deriving hydrophobicity values of amino acids utilize either sets of designed synthetic peptides or extended random datasets often extracted from proteomics experiments. We find that the best examples of these two methods provide virtually identical results--with exception of Lys, Arg, and His. The intrinsic hydrophobicity values of the remaining residues as determined by Kovacs et al. (Biopolymers 84 (2006) 283) correlates with an R(2)-value of 0.995+ against amino acid retention coefficients from our Sequence Specific Retention Calculator model (Anal. Chem. 78 (2006) 7785). This novel finding lays the foundation for establishing consensus amino acids hydrophobicity scales as determined by RP-HPLC. Simultaneously, we find the assignment of hydrophobicity values for charged residues (Lys, Arg and His at pH 2) is ambiguous; their retention contribution is strongly affected by the overall peptide hydrophobicity. The unique behavior of the basic residues is related to the dualistic character of the RP peptide retention mechanism, where both hydrophobic and ion-pairing interactions are involved. We envision the introduction of "sliding" hydrophobicity scales for charged residues as a new element in peptide retention prediction models. We also show that when using a simple additive retention prediction model, the "correct" coefficient value optimization (0.98+ correlation against values determined by synthetic peptide approach) requires a training set of at least 100 randomly selected peptides.     

Probing Gallate-Mediated Selectivity and High-Affinity Binding of Epigallocatechin Gallate: a Way-Forward in the Design of Selective Inhibitors for Anti-apoptotic Bcl-2 Proteins

Selective inhibition is a key focus in the design of chemotherapeutic compounds that can abrogate the oncogenic activities of anti-apoptotic Bcl-2 proteins. Although recent efforts have led to the development of highly selective BH3 mimetics, setbacks such as toxicities have limited their use in cancer therapy. Epigallocatechingallate (EGCG) has been widely reported to selectively inhibit Bcl-2 and Bcl-xL compared to other green tea phenols due to its gallate group. Herein, we investigate the interaction dynamics of EGCG at the hydrophobic grooves of Bcl-2 and Bcl-xL and the consequential effects on their BH4 domains. Arg143 and Asp108 (Bcl-2), and Glu96 and Tyr195 (Bcl-xL) formed high-affinity hydrogen interactions with the gallate group while non-gallate groups of EGCG formed weak interactions. EGCG-bound proteins showed systemic perturbations of BH4 domains coupled with the burial of crucial surface-exposed residues such as Lys17 (Bcl-2) and Asp11 (Bcl-xL); hence, a distortion of non-canonical domain interactions. Interactions of gallate group of EGCG with key hydrophobic groove residues underlie EGCG selectivity while concurrent BH4 domain perturbations potentiate EGCG inhibitory activities. Findings will aid the optimization and design of selective inhibitors that could suppress anti-apoptotic activities of Bcl2-family proteins with minimal toxicities.

     

Intracellular Self‐Assembly of Taxol Nanoparticles for Overcoming Multidrug Resistance

Multidrug resistance (MDR) remains the biggest challenge in treating cancers. Herein we propose the intracellular self‐assembly of nanodrugs as a new strategy for overcoming MDR. By employing a biocompatible condensation reaction, we rationally designed a taxol derivative Ac‐Arg‐Val‐Arg‐Arg‐Cys(StBu)‐Lys(taxol)‐2‐cyanobenzothiazole (CBT‐Taxol) which could be subjected to furin‐controlled condensation and self‐assembly of taxol nanoparticles (Taxol‐NPs). In vitro and in vivo studies indicated that, compared with taxol, CBT‐Taxol showed a 4.5‐fold or 1.5‐fold increase in anti‐MDR effects, respectively, on taxol‐resistant HCT 116 cancer cells or tumors without being toxic to the cells or the mice. Our results demonstrate that structuring protease‐susceptible agents and assembling them intracellularly into nanodrugs could be a new optimal strategy for overcoming MDR.     

Protein structure information from mass spectrometry? Selective titration of arginine residues by sulfonates

Noncovalently bound complexes between basic sites of peptides/proteins and sulfonates are studied using Matrix Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry. Reactive sulfonate dyes such as Cibacron Blue F3G-A are known to bind to protonated amino groups on the exterior of a protein. In this work, we examine a wide range of other sulfonates with distinctly simpler structure and more predictable reactivity. Naphthalene-sulfonic acid derivatives were found to bind to arginine only, as opposed to expected binding to all basic sites (Arg, Lys and His). Detailed control experiments were designed to unambigously confirm this selectivity and to rule out nonspecific adduct formation in the gas phase. The data show that the number of complex adducts found equals the number of accessible arginine sites on the surface of folded peptides and proteins, plus the N-terminus. Lys and His are not complexed nor are buried residues with hindered access. MALDI-MS can therefore provide fast information related to the exposed surface of these biomolecules. Additional titration experiments with 1-anilino-naphthalene-8-sulfonic acid (ANS) revealed that this fluorescent dye, which was often hypothesized to bind to so-called molten globule states of proteins, behaved exactly like all other naphthalene-sulfonic acids. ANS binding thus occurs largely through the sulfonate group.     

Essential of Proline and Valine Residues in the Peptide Derived from Lactoferrin for Angiotensin Converting Enzyme Inhibition

We synthesized Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu, the peptide contained in lactoferrin (Lf), to identify the angiotensin converting enzyme (ACE) inhibition. In an attempt to know the structure‐activity relationship of this peptide, we replaced Pro (the third amino acid residues from N‐terminal) or Val (the fourth amino acid residues from N‐terminal) with Ala (neutral amino acid), Glu (acidic amino acid) or Lys (basic amino acid) to produce six peptides. From the in vitro ACE inhibition (IC₅₀) of these synthesized peptides, the original peptide (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu) showed higher ACE inhibition than the replaced six peptides. Thus, replacement of Pro at the third amino acid residues or Val at the fourth position with Ala, Glu or Lys revealed the ACE inhibition to be lower than the original form of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu. Otherwise, we added one peptide at the C‐terminal of Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu and found both products with an addition of Val (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Val) or Ile (Leu‐Arg‐Pro‐Val‐Ala‐Ala‐Glu‐Ile) showing a lower ACE inhibition than the original one. The ACE inhibitions produced by both replaced peptides were without significance. Also, deletion of the last peptide at the C‐terminal (Leu‐Arg‐Pro‐Val‐Ala‐Ala) failed to produce a marked change of ACE inhibition as compared to the original one. These results suggest that Pro and Val are essential in the peptide for inhibition of ACE activity.     

N‐Methylation of Peptides and Proteins: An Important Element for Modulating Biological Functions

N‐Methylation is one of the simplest chemical modifications often occurring in peptides and proteins of prokaryotes and higher eukaryotes. Over years of evolution, nature has employed N‐methylation of peptides as an ingenious technique to modulate biological function, often as a mode of survival through the production of antibiotics. This small structural change can not only mobilize large protein complexes (as in the histone methylation), but also inhibits the action of enzymes by selective recognition of protein–protein interaction surfaces. In recent years through the advancement in synthetic approaches, the potential of N‐methylation has begun to be revealed, not only in modulating biological activity and selectivity as well as pharmacokinetic properties of peptides, but also in delivering novel drugs. Herein, we summarize the current knowledge of the versatility of N‐methylation in modulating biological, structural, and pharmacokinetic properties of peptides.     

Mass spectrometry‐based proteomics of oxidative stress: Identification of 4‐hydroxy‐2‐nonenal (HNE) adducts of amino acids using lysozyme and bovine serum albumin as model proteins

Modification of proteins by 4‐hydroxy‐2‐nonenal (HNE), a reactive by‐product of ω6 polyunsaturated fatty acid oxidation, on specific amino acid residues is considered a biomarker for oxidative stress, as occurs in many metabolic, hereditary, and age‐related diseases. HNE modification of amino acids can occur either via Michael addition or by formation of Schiff‐base adducts. These modifications typically occur on cysteine (Cys), histidine (His), and/or lysine (Lys) residues, resulting in an increase of 156 Da (Michael addition) or 138 Da (Schiff‐base adducts), respectively, in the mass of the residue. Here, we employed biochemical and mass spectrometry (MS) approaches to determine the MS “signatures” of HNE‐modified amino acids, using lysozyme and BSA as model proteins. Using direct infusion of unmodified and HNE‐modified lysozyme into an electrospray quadrupole time‐of‐flight mass spectrometer, we were able to detect up to seven HNE modifications per molecule of lysozyme. Using nanoLC‐MS/MS, we found that, in addition to N‐terminal amino acids, Cys, His, and Lys residues, HNE modification of arginine (Arg), threonine (Thr), tryptophan (Trp), and histidine (His) residues can also occur. These sensitive and specific methods can be applied to the study of oxidative stress to evaluate HNE modification of proteins in complex mixtures from cells and tissues under diseased versus normal conditions.     

Functionally orthogonal ligand-receptor pairs for the selective regulation of gene expression generated by manipulation of charged residues at the ligand-receptor interface of ER alpha and ER beta

The reengineering of protein-small molecule interfaces represents a powerful tool of chemical biology. For many applications it is necessary to engineer receptors so that they do not interact with their endogenous ligands but are highly responsive to designed ligand analogues, which in turn do not interact with endogenous proteins. The chemical design strategy used to reengineer protein-small molecule interfaces is particularly challenging for interfaces involving relatively plastic receptor binding sites and therefore presents a unique challenge in molecular design. In this study we explore the scope and limitations of a new strategy for manipulating polar/charged residues across the ligand receptor interface of estradiol (E2) and the estrogen receptor (ER). Carboxylate-functionalized E2 analogues can activate ER alpha(Glu353-->Ala) and ER beta(Glu305-->Ala) with very large selectivites, demonstrating that this design strategy is extendable to other members of the steroid hormone receptor family. Neutral E2 analogues were found to complement ER alpha(E353A) with similar potencies but with generally lower selectivities. This suggests that the high selectivity observed with ligand-receptor pairs generated by exchanging charged residues across ligand-receptor interfaces is only due in part to their complementary shapes and that appropriate introduction of charged functionality on the ligand can provide substantial enhancement of selectivity by decreasing the engineered ligands affinity for the endogenous receptor. Attempts to modify the cationic residues by complementing Arg394-->Ala or Arg394-->Glu were not successful.     

ZnZrOx-HZSM-5双功能催化剂催化甲苯与合成气烷基化制对二甲苯

作为重要的有机化工原料,近些年来随着聚酯行业的高速发展,对二甲苯(PX)需求量逐年增高.目前,PX主要通过传统的石油路线生产,例如石脑油催化重整、甲苯歧化和C₈芳烃异构化,这些路线的后续精馏能耗较高.甲醇作为碳源与甲苯烷基化制备PX有效提高了目标产物的选择性,且已实现工业化.然而,由于甲醇生成甲氧基烷基化物种的能垒较高,使反应温度较高,促进了甲醇制烯烃(MTO)副反应的进行,降低了甲醇利用率;且由于积炭的形成,催化剂容易失活.合成气是非石油基资源如煤炭、天然气和生物质等利用的重要平台,在转化为醇类、烯烃以及芳烃路径中将经过甲氧基中间体,因此,本文研发以合成气代替甲醇与甲苯烷基化制备PX的催化剂和催化过程.基于本课题组关于CO₂加氢耦合甲苯烷基化制PX的研究基础,本文将ZnZrO_x(ZZO)与ZSM-5(Z5)混合制得双功能催化剂,用于合成气转化耦合甲苯烷基化制PX.研究结果表明,通过优化催化剂的组成和烷基化反应条件,调控CO加氢反应和甲苯烷基化反应的匹配性,在甲苯转化率为10.3%时,可获得64.8%的二甲苯选择性(不计水煤气变换反应),其中PX占81.8%,气态烃副产物的选择性为10.9%;在相同条件下采用甲醇为烷基化试剂时,二甲苯选择性仅38.5%,其中PX占38.8%,此时气态烃副产物的选择性达26.2%.同位素效应实验结果表明,二甲苯中新增甲基来自于合成气,而非甲苯的歧化反应.催化剂构效研究结果表明,PX的选择性与分子筛孔径、酸性强度以及Br?nsted酸性位点有关;原位红外结果也证实了该反应呈现逆同位素效应(k_H2/k_D2=0.92),表明反应中甲酸盐物种(HCOO*)加氢可能是反应的决速步骤.与传统的甲醇甲苯烷基化路径相比,采用来源广泛和成本较低的合成气与甲苯进行烷基化反应的温度(340℃)更低,有效避免了MTO副反应的发生,同时,该催化剂可在100 h内保持良好稳定性.综上,本工作结果为高效制备高值芳烃PX提供了新思路.     

ZnZrOx-HZSM-5双功能催化剂催化甲苯与合成气烷基化制对二甲苯

作为重要的有机化工原料,近些年来随着聚酯行业的高速发展,对二甲苯(PX)需求量逐年增高.目前,PX主要通过传统的石油路线生产,例如石脑油催化重整、甲苯歧化和C₈芳烃异构化,这些路线的后续精馏能耗较高.甲醇作为碳源与甲苯烷基化制备PX有效提高了目标产物的选择性,且已实现工业化.然而,由于甲醇生成甲氧基烷基化物种的能垒较高,使反应温度较高,促进了甲醇制烯烃(MTO)副反应的进行,降低了甲醇利用率;且由于积炭的形成,催化剂容易失活.合成气是非石油基资源如煤炭、天然气和生物质等利用的重要平台,在转化为醇类、烯烃以及芳烃路径中将经过甲氧基中间体,因此,本文研发以合成气代替甲醇与甲苯烷基化制备PX的催化剂和催化过程.基于本课题组关于CO₂加氢耦合甲苯烷基化制PX的研究基础,本文将ZnZrO_x(ZZO)与ZSM-5(Z5)混合制得双功能催化剂,用于合成气转化耦合甲苯烷基化制PX.研究结果表明,通过优化催化剂的组成和烷基化反应条件,调控CO加氢反应和甲苯烷基化反应的匹配性,在甲苯转化率为10.3%时,可获得64.8%的二甲苯选择性(不计水煤气变换反应),其中PX占81.8%,气态烃副产物的选择性为10.9%;在相同条件下采用甲醇为烷基化试剂时,二甲苯选择性仅38.5%,其中PX占38.8%,此时气态烃副产物的选择性达26.2%.同位素效应实验结果表明,二甲苯中新增甲基来自于合成气,而非甲苯的歧化反应.催化剂构效研究结果表明,PX的选择性与分子筛孔径、酸性强度以及Br?nsted酸性位点有关;原位红外结果也证实了该反应呈现逆同位素效应(k_H2/k_D2=0.92),表明反应中甲酸盐物种(HCOO*)加氢可能是反应的决速步骤.与传统的甲醇甲苯烷基化路径相比,采用来源广泛和成本较低的合成气与甲苯进行烷基化反应的温度(340℃)更低,有效避免了MTO副反应的发生,同时,该催化剂可在100 h内保持良好稳定性.综上,本工作结果为高效制备高值芳烃PX提供了新思路.     

Selective Solid–Liquid and Liquid–Liquid Extraction of Lithium Chloride Using Strapped Calix[4]pyrroles

LiCl is a classic “hard” ion salt that is present in lithium‐rich brines and a key component in end‐of‐life materials (that is, used lithium‐ion batteries). Its isolation and purification from like salts is a recognized challenge with potential strategic and economic implications. Herein, we describe two ditopic calix[4]pyrrole‐based ion‐pair receptors ( 2 and 3 ), that are capable of selectively capturing LiCl. Under solid–liquid extraction conditions, using 2 as the extractant, LiCl could be separated from a NaCl/KCl salt mixture containing as little as 1 % LiCl with circa 100 % selectivity, while receptor 3 achieved similar separations when the LiCl level was as low as 200 ppm. Under liquid–liquid extraction conditions using nitrobenzene as the non‐aqueous phase, the extraction preference displayed by 2 is KCl>NaCl>LiCl. In contrast, 3 exhibits high selectivity towards LiCl over NaCl and KCl, with no appreciable extraction being observed for the latter two salts.     

Quantitative analysis of the effect of salt concentration on enzymatic catalysis.

Like pH, salt concentration can have a dramatic effect on enzymatic catalysis. Here, a general equation is derived for the quantitative analysis of salt-rate profiles: k(cat)/K(M) = (k(cat)/K(M))(MAX)/[1+([Na+]/K[Na+])(n')], where (k(cat)/K(M))(MAX) is the physical limit of k(cat)/K(M), K(Na+) is the salt concentration at which k(cat)/K(M) = (k(cat)/K(M))(MAX)/2, and -n' is the slope of the linear region in a plot of log(k(cat)/K(M)) versus log [Na+]. The value of n' is of special utility, as it reflects the contribution of Coulombic interactions to the uniform binding of the bound states. This equation was used to analyze salt effects on catalysis by ribonuclease A (RNase A), which is a cationic enzyme that catalyzes the cleavage of an anionic substrate, RNA, with k(cat)/K(M) values that can exceed 10(9) M(-1) s(-1). Lys7, Arg10, and Lys66 comprise enzymic subsites that are remote from the active site. Replacing Lys7, Arg10, and Lys66 with alanine decreases the charge on the enzyme as well as the value of n'. Likewise, decreasing the number of phosphoryl groups in the substrate decreases the value of n'. Replacing Lys41, a key active-site residue, with arginine creates a catalyst that is limited by the chemical conversion of substrate to product. This change increases the value of n', as expected for a catalyst that is more sensitive to changes in the binding of the chemical transition state. Hence, the quantitative analysis of salt-rate profiles can provide valuable insight into the role of Coulombic interactions in enzymatic catalysis.     

Engineering strategy to improve peptide analogs: from structure-based computational design to tumor homing

We present a chemical strategy to engineer analogs of the tumor-homing peptide CREKA (Cys-Arg-Glu-Lys-Ala), which binds to fibrin and fibrin-associated clotted plasma proteins in tumor vessels (Simberg et al. in Proc Natl Acad Sci USA 104:932–936, 2007) with improved ability to inhibit tumor growth. Computer modeling using a combination of simulated annealing and molecular dynamics were carried out to design targeted replacements aimed at enhancing the stability of the bioactive conformation of CREKA. Because this conformation presents a pocket-like shape with the charged groups of Arg, Glu and Lys pointing outward, non-proteinogenic amino acids α-methyl and N-methyl derivatives of Arg, Glu and Lys were selected, rationally designed and incorporated into CREKA analogs. The stabilization of the bioactive conformation predicted by the modeling for the different CREKA analogs matched the tumor fluorescence results, with tumor accumulation increasing with stabilization. Here we report the modeling, synthetic procedures, and new biological assays used to test the efficacy and utility of the analogs. Combined, our results show how studies based on multi-disciplinary collaboration can converge and lead to useful biomedical advances.     

Oligomeric Hydrogels Self‐Assembled from Reduction‐Controlled Condensation

Polymer hydrogels and small‐molecule‐based (SMB) supramolecular hydrogels have been widely explored. But oligomeric hydrogels have remained a challenge because synthetic difficulties of the oligomers and control of their amphiphilicities. Reported herein is the rational design of two precursors Cys(SEt)‐Lys‐CBT ( 1 ) and (Cys‐Lys‐CBT)₂ ( 2 ) (CBT=2‐cyano‐6‐aminobenzothiazole) and the use of a biocompatible condensation to prepare oligomeric hydrogels. Glutathione reduction of 1 or 2 yields the same gelator Cys‐Lys‐CBT ( 3 ) which condenses with each other to yield amphiphilic cyclic oligomers. The oligomers instantly self‐assemble into nanofibers and form oligomeric hydrogels with similar mechanic properties. Chemical analyses indicated that the major condensation product in both two hydrogels is a cyclic dimer. Considering its biocompatibility, optimal mechanical strength, and biodegradability, we believe that our oligomeric hydrogel might be useful for long‐term drug delivery in the future.     

Amino acid selective cross-saturation method for identification of proximal residue pairs in a protein-protein complex

We describe an NMR-based approach, the amino acid selective cross-saturation (ASCS) method, to identify the pairs of the interface residues of protein-protein complexes. ASCS uses a "cross-saturation (CS)-donor" protein, in which only one amino acid is selectively (1)H-labeled in a (2)H-background, and a "CS-acceptor" protein with uniform (2)H, (15)N labeling. Irradiation of the (1)H-labeled amino acid, which exists only in the donor, decreases the intensity of the (1)H- (15)N HSQC signals of the acceptor residues proximal to the (1)H-labeled CS-source residue(s) through the CS phenomenon. Given the three-dimensional structure of each protein in the complex, but not the complex structure, the combinatorial analysis of multiple ASCS results specify the CS-source residue(s), based on the spatial complementarity between the CS-source residues on the CS donor and the cross-saturated amide protons on the acceptor. NMR investigations of the labeling selectivity and efficiency in an E. coli host, which are critical for ASCS, revealed that Ala, Arg, His, Ile, Leu, Lys, Met, Phe, Pro, Trp, and Tyr are selectively labeled with a high (1)H/(2)H ratio. The observation of the ASCS was then confirmed using the known structure of the yeast ubiquitin (Ub) and yeast ubiquitin hydrolase 1 (YUH1). Conversely, reasonable candidates for the CS-source residues were suggested by the analysis of the ASCS results, with reference to the individual structures of YUH1 and Ub. The pairwise distance information between the CS-source residues and the cross-saturated amide groups obtained by ASCS will be useful for modeling protein-protein complexes.