Replacement of isobutyl by trifluoromethyl in pepstatin A selectively affects inhibition of aspartic proteinases

Two bis-trifluoromethyl pepstatin A analogues, carboxylic acid 1 and its methyl ester 2, have been synthesised in order to probe the properties and size of the trifluoromethyl (Tfm) group and compare it to the "bigger" isobutyl that is present in pepstatin A. The results demonstrate that Tfm can effectively replace the isobutyl chain as far as inhibitory activity against plasmepsin II (PM II), an aspartic proteinase from Plasmodium falciparum, is concerned. On the other hand, replacement of isobutyl by Tfm selectively affected activity against other aspartic proteinases tested. Two lines of evidence led to these conclusions. Firstly, compounds 1 and 2 retained single-digit nanomolar inhibitory activity against PM II, but were markedly less active against PM IV, cathepsin D and cathepsin E. Secondly, the X-ray crystal structures of the three complexes of PM II with 1, 2 and pepstatin A were obtained at 2.8, 2.4 and 1.7 A resolution, respectively. High overall similarity among the three complexes indicated that the central Tfm was well accommodated in the lipophilic S1 pocket of PM II, where it was involved in tight hydrophobic contacts. The interaction of PM II with Phe111 appeared to be crucial. Comparison of the crystal structures presented here, with X-ray structures or structural models of PM IV and cathepsin D, allowed an interpretation of the inhibition profiles of pepstatin A and its Tfm variants against these three enzymes. Interactions of the P1 side chain with amino acids that point into the S1 pocket appear to be critical for inhibitory activity. In summary, Tfm can be used to replace an isobutyl group and can affect the selectivity profile of a compound. These findings have implications for the design of novel bioactive molecules and synthetic mimics of natural compounds.     

3- Instead of 4-helix formation in a de novo designed protein in solution revealed by small-angle X-ray scattering

De novo design and chemical synthesis of proteins and their mimics are central approaches for understanding protein folding and accessing proteins with novel functions. We have previously described carbohydrates as templates for the assembly of artificial proteins, so-called carboproteins. Here, we describe the preparation and structural studies of three alpha-helical bundle carboproteins, which were assembled from three different carbohydrate templates and one amphiphilic hexadecapeptide sequence. This heptad repeat peptide sequence has been reported to lead to 4-alpha-helix formation. The low resolution solution structures of the three carboproteins were analyzed by means of small-angle X-ray scattering (SAXS) and synchrotron radiation circular dichroism (SRCD). The ab initio SAXS data analysis revealed that all three carboproteins adopted an unexpected 3+1-helix folding topology in solution, while the free peptide formed a 3-helix bundle. This finding is consistent with the calculated alpha-helicities based on the SRCD data, which are 72 and 68 % for two of the carboproteins. The choice of template did not affect the overall folding topology (that is for the 3+1 helix bundle) the template did have a noticeable impact on the solution structure. This was particularly evident when comparing 4-helix carboprotein monomers with the 2x2-helix carboprotein dimer as the latter adopted a more compact conformation. Furthermore, the clear conformational differences observed between the two 4-helix (3+1) carboproteins based on D-altropyranoside and D-galactopyranoside support the notion that folding is affected by the template, and subtle variations in template distance-geometry design may be exploited to control the solution fold. In addition, the SRCD data show that template assembly significantly increases thermostability.     

The Characteristic Structure of Anti‐HIV Actinohivin in Complex with Three HMTG D1 Chains of HIV‐gp120

The anti‐HIV lectin actinohivin (AH) specifically interacts with HMTG (high‐mannose‐type glycan), which is attached to the glycoprotein gp120 of HIV‐1 in a process in which the three branched mannotriose chains (D1, D2, and D3) of HMTG exhibit different binding affinities, it being estimated that that of D1 is the strongest, that of D3 is weaker, and that of D2 is undetectable. These properties have been ascribed to the stereochemical differences in linkages between the second and the third mannose residues of the three chains. In order to clarify the interaction geometry between AH and the major target D1, an X‐ray determination of the crystal structure of AH in complex with D1—which is α(1,2)mannotriose composed of three mannose (Man) residues linked together only by α(1,2) bonding—has been performed. In each of the three D1‐binding pockets of AH, two Man residues of D1 are accommodated at zones 1 and 2 in the pocket, in the same way as those found in the α(1,2)mannobiose‐bound AH crystals. However, an OMIT map shows poor densities at both ends of the two residues. This suggests the existence of positional disorder of D1 in the pocket: the two zones are each occupied by two Man residues in two different modes, with mode A involving the Man1 and Man2 residues and mode B the Man2 and Man3 residues. In each mode, D1 is stabilized by adopting a double‐bracket‐shaped conformation through C?H ??? O interactions. In mode B, however, the Man1 residue, which is the most sensitive residue to AH binding, protrudes wholly into the solvent region without contacts with AH. In mode A, in contrast, the Man3 residue interacts with the essential hydrophobic amino acid residues (Tyr and Leu conserved between the three pockets) of AH. Therefore, mode A is likely to be the one that occurs when whole HMTG is bound. In this mode, the two hydroxy groups (O3 and O4) of the Man2 residue are anchored in zone 2 by four hydrogen bonds with Asp, Asn, and Tyr residues of AH. In addition, it has been found that an isolated water molecule buried in the hydrophobic long loop bridges between Asp of AH and the hydroxy group of Man2 through hydrogen bonds. The most interesting feature is found in the interaction of the Man1 and Man3 residues with AH. All eight hydroxy groups of the two residues are completely exposed in the solvent region, whereas their hydrophobic parts make contacts with a Leu residue and two Tyr residues so that the shape of D1 and the surface of AH fit well over a wide area. These structural characteristics are potentially useful for development of AH to produce more effective antiretroviral drugs to suppress the infectious expansion of HIV/AIDS and to help expedite an end to the HIV/AIDS pandemic in the near future.     

Lamellar arrangements of linear polyethylene in ultrathin films

The crystal orientations of linear polyethylene films on silicon substrates are investigated using grazing incidence X‐ray diffraction and atomic force microscopy. From diffraction analysis, we can identify the structural arrangement of PE crystals in ultrathin film. The orientation of lamellar crystal in PE films changes from edge‐on to flat‐on with the decrease of film thickness in the film thickness below ～ 100 nm. The slightly inclined lamellae relative to the substrate are found to coexist with the flat‐on lamellae in thin PE films that we have investigated. We find that the crystal orientation and structures is governed by the constraint imposed by film thickness rather than enthalpy gain as the film got thinner especially in the thickness below 200 nm. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012     

Characterization of soybean protein concentrate—stearic acid/palmitic acid blend edible films

The effect of incorporating commercial stearic acid/palmitic acid blend (SA/PA, 63/37 wt %) into hydrophilic soybean protein concentrate (SPC) film‐forming solutions at neutral and alkaline pH on some selected properties of edible cast films was investigated. SA/PA‐added SPC film exhibited a significant increase in translucency, being more relevant for films obtained at pH 7. This was associated with the more heterogeneous morphology of such films as observed by scanning electron microscopy. Calorimetric measurements and X‐ray diffraction studies confirmed the presence of crystalline fatty acids in films at pH 7 and new crystalline structures at pH 10 due to interactions or reactions between SPC and SA/PA blend. Fourier Transform infrared spectroscopy results confirmed the incorporation of fatty acids into SPC and revealed the occurrence of interactions between both components, depending on the film‐forming emulsion pH. Moisture absorption isotherms at high relative humidity (RH) were determined and experimental data were adequately fitted by Peleg's empirical equation. Control SPC films produced at pH 7 were distinctly more moisture resistant than those at pH 10 owing to the more charged protein molecules at alkaline pH. The increased moisture resistance of SA/PA‐added‐SPC film at pH 10 was related to the more homogeneous dispersion of fatty acid particles within the protein matrix. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012     

Preparation of nanosize polyaniline by solid‐state polymerization and determination of crystal structure

BACKGROUND: Nanosize polyaniline has several advantages in both the fabrication of nanodevices and for preparing nanoscale electrical connections in highly conducting polymer composites. RESULTS: Nanosize polyaniline with a diameter of 30–60 nm was prepared using a solid‐state polymerization process (PANI‐S) by mixing an equimolar quantity of ammonium persulfate and anilinium chloride crystals with a mortar and pestle. Polyaniline was also synthesized using a conventional oxidative polymerization method (PANI‐C) in an aqueous medium for comparison. Conductivity and contact angle measurements, infrared spectroscopy, ultraviolet spectroscopy, transmission electron microscopy and thermogravimetric analysis were carried out. An in‐depth investigation of the crystal structure of these polymers was carried out through powder X‐ray diffraction analysis. CONCLUSION: PANI‐S exhibited lower conductivity due to the presence of less emeraldine base form, lower crystallinity, greater d‐spacing and greater inter‐chain separation than PANI‐C. The hydrophilicity and thermal stability of PANI‐S were higher than those of PANI‐C. The unit cell volume of PANI‐S was much higher, resulting in a larger crystallite size and a greater number of atoms in the unit cell than PANI‐C. Copyright © 2009 Society of Chemical Industry     

The Structure of Glycerol Trinitrate Reductase NerA from Agrobacterium radiobacter Reveals the Molecular Reason for Nitro‐ and Ene‐Reductase Activity in OYE Homologues

In recent years, Old Yellow Enzymes (OYEs) and their homologues have found broad application in the efficient asymmetric hydrogenation of activated C?C bonds with high selectivities and yields. Members of this class of enzymes have been found in many different organisms and are rather diverse on the sequence level, with pairwise identities as low as 20 %, but they exhibit significant structural similarities with the adoption of a conserved (αβ)₈‐barrel fold. Some OYEs have been shown not only to reduce C?C double bonds, but also to be capable of reducing nitro groups in both saturated and unsaturated substrates. In order to understand this dual activity we determined and analyzed X‐ray crystal structures of NerA from Agrobacterium radiobacter, both in its apo form and in complex with 4‐hydroxybenzaldehyde and with 1‐nitro‐2‐phenylpropene. These structures, together with spectroscopic studies of substrate binding to several OYEs, indicate that nitro‐containing substrates can bind to OYEs in different binding modes, one of which leads to C?C double bond reduction and the other to nitro group reduction.     

The ATP/ADP Substrate Specificity Switch between Toxoplasma gondii NTPDase1 and NTPDase3 is Caused by an Altered Mode of Binding of the Substrate Base

Two nucleoside triphosphate diphosphohydrolase isoforms (NTPDase1 and NTPDase3) are responsible for the hydrolysis of nucleotides by the intracellular protozoan Toxoplasma gondii. They constitute about 3 % of the total parasite protein. Despite sharing 97 % sequence identity they exhibit opposite ATP versus ADP substrate discrimination ratios. Here we show by mutagenesis that the residues G492/G493 in NTPDase3 and R492/E493 in NTPDase1 are predominantly responsible for the differences in substrate specificity. Crystal structures of NTPDase1 in complexation with analogues of ATP and ADP reveal that the inverted substrate specificity of NTPDase1 relative to NTPDase3 is achieved by switching from the canonical substrate binding mode to a very different alternative one. Instead of being stacked on top of a helix of the C‐terminal domain the nucleotide base is positioned in the interdomain space between the side chains of R108 and R492, recruited from both domains. Furthermore, we show that the NTPDase1 substrate specificity is mainly dependent on the presence of the side chain of E493, which causes repositioning of the ribose component of the nucleotide. All in all, binding by the flexible side chains in the alternative binding mode in NTPDase1 allows for equally good positioning of ATP and ADP with increased activity toward ADP relative to what is seen in the case of NTPDase3.     

Hedycaryol Synthase in Complex with Nerolidol Reveals Terpene Cyclase Mechanism

The biosynthesis of terpenes is catalysed by class I and II terpene cyclases. Here we present structural data from a class I hedycaryol synthase in complex with nerolidol, serving as a surrogate for the reaction intermediate nerolidyl diphosphate. This prefolded ligand allows mapping of the active site and hence the identification of a key carbonyl oxygen of Val179, a highly conserved helix break (G1/2) and its corresponding helix dipole. Stabilising the carbocation at the substrate's C1 position, these elements act in concert to catalyse the 1,10 ring closure, thereby exclusively generating the anti‐Markovnikov product. The delineation of a general mechanistic scaffold was confirmed by site‐specific mutations. This work serves as a basis for understanding carbocation chemistry in enzymatic reactions and should contribute to future application of these enzymes in organic synthesis.     

α‐Crystallin Modulates its Chaperone Activity by Varying the Exposed Surface

The α‐crystallin family of small heat shock proteins possesses chaperone activity in response to stress and is involved in several neurological, muscular, and ophthalmic pathologies. This family includes the vertebrate lens protein α‐crystallin, associated with cataract disease. In this study, by combining small‐angle X‐ray and light scattering techniques, the structure and shape of α‐crystallin was revealed in its native state and after a transition caused by heat stress. Below critical temperature (T_c), α‐crystallin appears as an ellipsoid with a central cavity; whereas at high temperatures the cavity almost disappears, and the protein rearranges its structure, increasing the solvent‐exposed surface while retaining the ellipsoidal symmetry. Contextually, at T_c, α‐crystallin chaperone binding shows an abrupt increase. By modelling the chaperone activity as the formation of a complex composed of α‐crystallin and an aggregating substrate, it was demonstrated that the increase of α‐crystallin‐exposed surface is directly responsible for its gain in chaperone functionality.     

A study on the preparation of polymer/montmorillonite nano‐composite materials by photo‐polymerization

The preparation of polymer/montmorillonite intercalation composite materials was studied by two kinds of photo‐polymerization reaction (photo‐acid generation and photo‐radical generation). Small‐angle X‐ray diffraction was used for the structural characterization of montmorillonite contained in the products. Results indicated that, after chemical modification of montmorillonite, the monomer (methyl methacrylate) and the prepolymer (m‐cresol/HMMM) were able to intercalate into the layers of clay and to polymerize ‘in situ’, thus producing photo‐polymerized composite materials. The advantages and shortcomings of the method of photo‐polymerization for the preparation of these composite materials are discussed. © 2001 Society of Chemical Industry     

The Tyrosine Gate of the Bacterial Lectin FimH: A Conformational Analysis by NMR Spectroscopy and X‐ray Crystallography

Urinary tract infections caused by uropathogenic E. coli are among the most prevalent infectious diseases. The mannose‐specific lectin FimH mediates the adhesion of the bacteria to the urothelium, thus enabling host cell invasion and recurrent infections. An attractive alternative to antibiotic treatment is the development of FimH antagonists that mimic the physiological ligand. A large variety of candidate drugs have been developed and characterized by means of in vitro studies and animal models. Here we present the X‐ray co‐crystal structures of FimH with members of four antagonist classes. In three of these cases no structural data had previously been available. We used NMR spectroscopy to characterize FimH–antagonist interactions further by chemical shift perturbation. The analysis allowed a clear determination of the conformation of the tyrosine gate motif that is crucial for the interaction with aglycone moieties and was not obvious from X‐ray structural data alone. Finally, ITC experiments provided insight into the thermodynamics of antagonist binding. In conjunction with the structural information from X‐ray and NMR experiments the results provide a mechanism for the often‐observed enthalpy–entropy compensation of FimH antagonists that plays a role in fine‐tuning of the interaction.     

Highly effective protease inhibitors from variants of human pancreatic secretory trypsin inhibitor (hPSTI): an assessment of 3-D structure-based protein design

The results of a protein design project are used to comparedifferent predictive strategies with respect to proteinproteininteractions. We have been able to generate variants of humanpancreatic secretory trypsin inhibitor (hPSTI) optimized withrespect to the affinity and specificity for human leukocyteelastase relative to trypsin and chymotrypsin, and in particularchymotrypsin. The extremely strong and specific human leukocyteelastase inhibitors were thus developed in three rounds of mutagenesisand two rounds of 3-D modelling; only 24 variants in total weresynthesized, although variations at seven different amino acidpositions were involved (i.e. from 20⁷ possible variants). Anexcellent elastase inhibitor could be designed with the minimumof two amino acid exchanges. The value of structural modellingand actual structure determination is discussed in the lightof the experimental results of the designed protein variantsand the results of tertiary structure determinations of thefree variant and the inhibitorprotease complex. Particular referenceis given to the strategy to be followed in protein design projectsin general and to the development of protease inhibitors inparticular.     

Flameless Combustion Synthesis of Ni and Ag Nanoparticles in Ballasted Systems: A Time‐Resolved X‐ray Diffraction Study

The combustion of cellulose nitrate in ballasted mixtures containing an organic binder and nickel hydroxycarbonate or silver carbonate as precursors resulted Ni or Ag nanoparticles. The formation of Ni and Ag nanoparticles from flameless combustion of cellulose nitrate was monitored by time‐resolved X‐ray diffraction. During the formation of the Ag nanoparticles, the diffraction patterns exhibited only signals from decreasing amounts of the precursor and newly simultaneously formed 20–30 nm silver particles. It was detected that in the systems with Ni precursor the formation of the Ni 5–10 nm crystals proceeded by some 2–3 s diffraction‐silent intermediate states of the whole system.     

A Fragment‐Based Approach to Probing Adenosine Recognition Sites by Using Dynamic Combinatorial Chemistry

A new strategy that combines the concepts of fragment‐based drug design and dynamic combinatorial chemistry (DCC) for targeting adenosine recognition sites on enzymes is reported. We demonstrate the use of 5′‐deoxy‐5′‐thioadenosine as a noncovalent anchor fragment in dynamic combinatorial libraries templated by Mycobacterium tuberculosis pantothenate synthetase. A benzyl disulfide derivative was identified upon library analysis by HPLC. Structural and binding studies of protein–ligand complexes by X‐ray crystallography and isothermal titration calorimetry informed the subsequent optimisation of the DCC hit into a disulfide containing the novel meta‐nitrobenzyl fragment that targets the pantoate binding site of pantothenate synthetase. Given the prevalence of adenosine‐recognition motifs in enzymes, our results provide a proof‐of‐concept for using this strategy to probe adjacent pockets for a range of adenosine binding enzymes, including other related adenylate‐forming ligases, kinases, and ATPases, as well as NAD(P)(H), CoA and FAD(H₂) binding proteins.