Size Of Side Chain Research Articles

Termination, Propagation, and Transfer Kinetics of Midchain Radicals in Methyl Acrylate and Dodecyl Acrylate Homopolymerization

Methyl acrylate (MA) and dodecyl acrylate (DA) homopolymerizations (1.5 M in toluene) were investigated via single pulse–pulsed laser polymerization in conjunction with detection of the type and of the concentration of radicals by electron paramagnetic resonance spectroscopy (SP–PLP–EPR). The evolution of secondary propagating (SPR) and midchain (MCR) radicals, after instantaneous laser-induced production of an intense burst of primary radicals, was measured with a time resolution of microseconds from 0 to 60 °C. With the kinetics of chain-length-dependent termination and of propagation for SPRs being already known from experiments at subzero temperature, the rate coefficients for the formation of MCRs from SPRs by backbiting, kbb, of propagation from MCRs, kpt, and of cross-termination between an SPR and an MCR, ktst, were deduced. The present paper aims at elucidating the impact of the size of the ester side chain on kbb, kpt, and ktst. In passing from MA to DA (in 1.5 M solution of toluene), the rate c...

NMR study of mutations of glycine-52 of the catalytic domain of diphtheria toxin

Cross-reacting-material 197 (CRM197) is a naturally occurring non-toxic mutant of diphtheria toxin (DT) that is one of the few carrier protein used in the manufacture of polysaccharide vaccines targeting bacterial pathogens such as Neisseria meningitidis, Streptococcus pneumaniae and Haemophilus influenzae. A detailed explanation in structural terms for the lack of toxicity has started to emerge with the report of the X-ray structure of CRM197. Here, we present an NMR spectroscopy study of the wild-type catalytic domain of diphtheria toxin and the effects of mutations at residue 52 on its conformation. We utilized a strategy that consisted of gradually inducing steric perturbations by increasing the side chain size of the residue. Results show that the catalytic domain does not tolerate even the smallest perturbation, such as a glycine to alanine substitution, resulting in the destabilization of domain fold leading to protein aggregation. The observed behavior is further exacerbated with the substitution of amino acids with larger side chains. These findings support the concept that the lack of toxicity observed for CRM197 is the result of a highly unstable conformation of its catalytic domain that, upon insertion into the cell, cannot properly refold and perform its catalytic activity responsible for the arrest of all cellular protein synthesis.

Primary Alkylphosphine–Borane Polymers: Synthesis, Low Glass Transition Temperature, and a Predictive Capability Thereof

With a multitude of potential applications, poly(phosphine–borane)s are an interesting class of polymer comprising main-group elements within the inorganic polymer backbone. A new family of primary alkylphosphine–borane polymers was synthesized by a solvent-free rhodium-catalyzed dehydrocoupling reaction and characterized by conventional chemicophysical techniques. The thermal stability of the polymers is strongly affected by the size and shape of the alkyl side chain with longer substituents imparting greater stability. The polymers show substantial stability toward UV illumination and immersion in water; however, they undergo a loss of alkylphosphine units during thermal degradation. The polymers exhibit glass transition temperatures (Tg) as low as −70 °C. A group interaction model (GIM) framework was developed to allow the semiquantitative prediction of Tg values, and the properties of the materials in this study were used to validate the model.

Front Cover Picture: A Structure‐Based Activity Study of Highly Active Unsymmetrically Substituted NHC Gold(I) Catalysts (Adv. Synth. Catal. 1/2018)

The front cover image, provided by Stephen Hashmi and co-workers, illustrates the results of their work on the synthesis and catalytic activity of saturated and unsaturated NHC as well as NHOC gold(I) complexes. The catalytic activity is strongly influenced by the type of ligand and by side-chain ring size. For the furane-yne cyclization the saturated NHC bearing a 15-membered ring as a side-chain is the match winner, as indicated by the position on the winners’ rostrum. The cover artist is Jasmin Schießl. Details of this work can be found in the full paper on pages 106–111 (P. Zargaran, T. Wurm, D. Zahner, J. Schießl, M. Rudolph, F. Rominger, A. S. K. Hashmi, Adv. Synth. Catal. 2018, 360, 106–111; DOI: 10.1002/adsc.201701080).

Peptide Self-Assembled Nanostructures with Distinct Morphologies and Properties Fabricated by Molecular Design.

Six surfactant-like peptides with the same amino acid composition but different primary sequences are designed, including G3A3V3I3K3, K3I3V3A3G3, I3V3A3G3K3, K3G3A3V3I3, V3G3I3A3K3, and K3A3I3G3V3. These peptides form antiparallel β-sheets during self-assembly. Because the constituent residues have different side chain size and hydrophobicity, sequence changes adjust group distribution and hydrophobicity on the two sides of a given β-sheet. This consequently tunes the binding energy of the side-to-side pairing conformations and leads to different self-assembled structures. G3A3V3I3K3 and K3I3V3A3G3 form short nanorods with diameters of 8.5 ± 1.0 nm and lengths <150 nm. I3V3A3G3K3 and K3G3A3V3I3 form nanosheets with heights of 4.0 ± 0.5 nm and limited lengths and widths. V3G3I3A3K3 and K3A3I3G3V3 form long fibrils with diameters of 7.0 ± 1.0 nm and lengths of micrometer scale. These nanostructures exhibit different capacity in encapsulating insoluble hydrophobic drug molecules and delivering them into the cells. The nanosheets of I3V3A3G3K3 and K3G3A3V3I3 can encapsulate both nile red and doxorubicin molecules to an extent of up to 17-23% in mole ratio. Moreover, the shape and size of the nanostructures affect the drug delivery into cells greatly, with the nanosheets and short rods exhibiting higher efficiency than the long fibrils. The study provides new insights into programmed peptide self-assembly toward specific functionalities.

Solid-liquid equilibrium and heat capacity trend in the alkylimidazolium PF6 series

The heat capacity and thermal behavior trend along the 1-alkyl-3-methylimidazolium hexafluorophosphate [CnC1im][PF6] (with n=2–10, 12) ionic liquids series, is used to explore the effect of the alkyl chain length in the nanostructuration. The heat capacities of the studied ILs were measured with an uncertainty better than ±0.15% and are in excellent agreement with the available data in the literature. An odd-even effect for the specific and volumic heat capacities of the [CnC1im][PF6] series was found. The observed odd-even effect in the liquid heat capacity was rationalized considering the preferential orientation of the terminal CH3 group. The higher specific/volumic heat capacities shown for the [C6C1im][PF6] and [C8C1im][PF6] are an indication of an additional conformational disorder increase in the liquid phase that could be related with a weaker alkyl chain interdigitation capability of the even number chain ILs. The melting temperatures and consequent ∆slHmo and ∆slSmo trend along the alkyl series present a V-shape profile that is explained based on the analysis of the balance between the initial decrease of the electrostatic interaction potential and the increase of the van der Waals interactions with the increasing size of the alkyl side chain of the cation. The inhibition of crystallization for intermediate alkyl chain size (from [C5C1im][PF6] to [C8C1im][PF6]) seems to arise from the overlapping of the hypothetical cold crystallization temperature by the melting temperature. Above the critical alkyl size, CAS, a regular increase in the entropy and enthalpy profiles presents a similar shape than the observed in other alkane series and is a strong support of the intensification of the ILs nanostructuration.

Using chirality to probe the conformational dynamics and assembly of intrinsically disordered amyloid proteins

Intrinsically disordered protein (IDP) conformers occupy large regions of conformational space and display relatively flat energy surfaces. Amyloid-forming IDPs, unlike natively folded proteins, have folding trajectories that frequently involve movements up shallow energy gradients prior to the “downhill” folding leading to fibril formation. We suggest that structural perturbations caused by chiral inversions of amino acid side-chains may be especially valuable in elucidating these pathways of IDP folding. Chiral inversions are subtle in that they do not change side-chain size, flexibility, hydropathy, charge, or polarizability. They allow focus to be placed solely on the question of how changes in amino acid side-chain orientation, and the resultant alterations in peptide backbone structure, affect a peptide’s conformational landscape (Ramachandran space). If specific inversions affect folding and assembly, then the sites involved likely are important in mediating these processes. We suggest here a “focused chiral mutant library” approach for the unbiased study of amyloid-forming IDPs.

Influence of Side Chain Sizes on Dielectric and Electrorheological Responses of Poly(ionic liquid)s.

Poly(ionic liquid)s (PILs) show potential as new anhydrous polyelectrolyte-based smart electrorheological (ER) materials. Understanding the structure-property relationship on a molecular level is very important for guiding the design of PIL-based ER materials. In this paper, a family of (p-vinylbenzyl)trialkylammonium hexafluorophosphate-based PIL particles containing different length of substituent alkyl chains attached to immobile ammonium charged site is synthesized for especially understanding the size effect of side chains on ER property. To exclude the particle shape effect, the PIL particles are controlled to be monodisperse sphere-like morphology with a similar size. The ER property of PIL particles when dispersed in insulating oil is investigated and compared by temperature-modulated rheological test under external electric fields. The dielectric spectroscopy is finally performed to study the mechanism behind the size effect of side chains on the ER property of PIL particles. We demonstrate that the size of side chains on the charged site has a significant impact on the ER effect of PIL particles and the PIL particles with shorter side chains have stronger ER property but degraded temperature dependence, and this is related to the fact that the variation of side chain size alters the transport dynamic of mobile counterions and ion motion-induced interfacial polarization.

The Dynameomics Entropy Dictionary: A Large-Scale Assessment of Conformational Entropy across Protein Fold Space.

Molecular dynamics (MD) simulations contain considerable information with regard to the motions and fluctuations of a protein, the magnitude of which can be used to estimate conformational entropy. Here we survey conformational entropy across protein fold space using the Dynameomics database, which represents the largest existing data set of protein MD simulations for representatives of essentially all known protein folds. We provide an overview of MD-derived entropies accounting for all possible degrees of dihedral freedom on an unprecedented scale. Although different side chains might be expected to impose varying restrictions on the conformational space that the backbone can sample, we found that the backbone entropy and side chain size are not strictly coupled. An outcome of these analyses is the Dynameomics Entropy Dictionary, the contents of which have been compared with entropies derived by other theoretical approaches and experiment. As might be expected, the conformational entropies scale linearly with the number of residues, demonstrating that conformational entropy is an extensive property of proteins. The calculated conformational entropies of folding agree well with previous estimates. Detailed analysis of specific cases identifies deviations in conformational entropy from the average values that highlight how conformational entropy varies with sequence, secondary structure, and tertiary fold. Notably, α-helices have lower entropy on average than do β-sheets, and both are lower than coil regions.

Separation and structural characterization of groups from a high-volatile bituminous coal based on multiple techniques

Although considerable progress has been made in revealing the coal macromolecular structure via solvent extraction, there remains a challenge in elucidating the coal structure due to low extraction yields of coal, poor selectivity of extraction solvents, and complexity of extracts. In this work, a high-volatile bituminous coal was successfully separated into seven groups (G1–G7) with less diversity within each class using multistep extraction followed by column chromatography. The total extraction yield (dmmf) reached up to 56% and the structural characteristics of the seven groups were identified and investigated with a series of analytical techniques. The results showed that the individual groups had a rather unique composition and their chemical properties were different in elemental composition, functional groups, aromatic cluster size, number and length of the alkyl side chains, and degree of order, which resulted in differences of their pyrolysis reactivities. Aliphatic hydrogen accounted for 99% of total hydrogen in n-heptane eluted fraction (G4) but the aliphatic degree in the extract residue (G1) was only 35.7%. The ratios of aromatic bridgehead carbon were 0.32, 0.30, and 0.27 for G1, CCl4 insoluble fraction (G2), and n-heptane insoluble fraction (G3), respectively. Additionally, total volatiles achieved 99.8, 98.1, 98.2, 89.0, and 60.0%, respectively during pyrolysis of G4, toluene eluted fraction (G5), ethyl acetate eluted fraction (G5), methanol eluted fraction (G7), and G3 at end temperature of 800°C, which were substantially higher than those for G1 and G2. In comparison with the partition of coal structure using maceral components, the proposed separation method provides an efficient and convenient investigating for structural exploration and these data can be combined to create structures that are cognitive of the structural diversity present. Through this, exploration of the complex conversion mechanism of coals would become more accessible during pyrolysis, gasification, liquefaction, and coking processes.

Optimization of a PEGylated Glucuronide-Monomethylauristatin E Linker for Antibody–Drug Conjugates

The emergence of antibody-drug conjugates (ADC), such as brentuximab vedotin and ado-trastuzumab emtansine, has led to increased efforts to identify new payloads and develop improved drug-linker technologies. Most antibody payloads impart significant hydrophobicity to the ADC, resulting in accelerated plasma clearance and suboptimal in vivo activity, particularly for conjugates with high drug-to-antibody ratios (DAR). We recently reported on the incorporation of a discrete PEG24 polymer as a side chain in a β-glucuronidase-cleavable monomethylauristatin E (MMAE) linker to provide homogeneous DAR 8 conjugates with decreased plasma clearance and increased antitumor activity in xenograft models relative to a non-PEGylated control. In this work, we optimized the drug-linker by minimizing the size of the PEG side chain and incorporating a self-stabilizing maleimide to prevent payload de-conjugation in vivo Multiple PEG-glucuronide-MMAE linkers were prepared with PEG size up to 24 ethylene oxide units, and homogeneous DAR 8 ADCs were evaluated. A clear relationship was observed between PEG length and conjugate pharmacology when tested in vivo Longer PEG chains resulted in slower clearance, with a threshold length of PEG8 beyond which clearance was not impacted. Conjugates bearing PEG of sufficient length to minimize plasma clearance provided a wider therapeutic window relative to faster clearing conjugates bearing shorter PEGs. A lead PEGylated glucuronide-MMAE linker was identified incorporating a self-stabilizing maleimide and a PEG12 side chain emerged from these efforts, enabling highly potent, homogeneous DAR 8 conjugates and is under consideration for future ADC programs. Mol Cancer Ther; 16(1); 116-23. ©2016 AACR.

Role of the Conserved Valine 236 in Access of Ligands to the Active Site of Thermus thermophilus ba3 Cytochrome Oxidase

Knowledge of the role of conserved residues in the ligand channel of heme-copper oxidases is critical for understanding how the protein scaffold modulates the function of these enzymes. In this study, we investigated the role of the conserved valine 236 in the ligand channel of ba3 cytochrome c oxidase from Thermus thermophilus by mutating the residue to a more polar (V236T), smaller (V236A), or larger (V236I, V236N, V236L, V236M, and V236F) residue. The crystal structures of the mutants were determined, and the effects of the mutations on the rates of CO, O2, and NO binding were investigated. O2 reduction and NO binding were unaffected in V236T, while the oxidation of heme b during O-O bond cleavage was not detected in V236A. The V236A results are attributed to a decrease in the rate of electron transfer between heme b and heme a3 during O-O bond cleavage in V236A, followed by faster re-reduction of heme b by CuA. This interpretation is supported by classical molecular dynamics simulations of diffusion of O2 to the active site in V236A that indicated a larger distance between the two hemes compared to that in the wild type and increased contact of heme a3 with water and weakened interactions with residues R444 and R445. As the size of the mutant side chain increased and protruded more into the ligand cavity, the rates of ligand binding decreased correspondingly. These results demonstrate the importance of V236 in facilitating access of ligands to the active site in T. thermophilus ba3.

Electron Transfer in Bacterial Reaction Centers with the Photoactive Bacteriopheophytin Replaced by a Bacteriochlorophyll through Coordinating Ligand Substitution

The influence of amino acid substitutions at position M214 (M-subunit, residue 214) on the rate and pathway of electron transfer involving the bacteriopheophytin cofactor, HA, in a bacterial photosynthetic reaction center has been explored in a series of Rhodobacter sphaeroides mutants. The M214 leucine (L) residue of the wild type was replaced with histidine (H), glutamine (Q), and asparagine (N), creating the mutants M214LH, M214LQ, and M214LN, respectively. As has been reported previously for M214LH, each of these mutations resulted in a bacteriochlorophyll molecule in place of a bacteriopheophytin in the HA pocket, forming so-called β-type mutants (in which the HA cofactor is called βA). In addition, these mutations changed the properties of the surrounding protein environment in terms of charge distribution and the amino acid side chain volume. Electron transfer reactions from the excited primary donor P to the acceptor QA were characterized using ultrafast transient absorption spectroscopic techniques. Similar to that of the previously characterized M214LH (β mutant), the strong energetic mixing of the P(+)BA(-) and P(+)βA(-) states (the mixed anion is denoted I(-)) increased the rate of charge recombination between P(+) and I(-) in competition with the I(-) → QA forward reaction. This reduced the overall yield of charge separation forming the P(+)QA(-) state. While the kinetics of the primary electron transfer forming P(+)I(-) were essentially identical in all three β mutants, the rates of the βA(-) (I(-)) → QA electron transfer in M214LQ and M214LH were very similar but quite different from that of the M214LN mutant. The observed yield changes and the differences in kinetics are correlated more closely with the volume of the mutated amino acid than with their charge characteristics. These results are consistent with those of previous studies of a series of M214 mutants with different sizes of amino acid side chains that did not alter the HA cofactor composition [Pan, J., et al. (2013) J. Phys. Chem. B 117, 7179-7189]. Both studies indicate that protein relaxation in this region of the reaction center plays a key role in stabilizing charge-separated states involving the HA or βA cofactor. The effect is particularly pronounced for reactions occurring on time scales of tens and hundreds of picoseconds (forward transfer to the QA and charge recombination).

Poly(esters) Containing Two Silicon Atoms and Aminoacidic Residues in the Main Chain: Synthesis, Characterization and Thermal Studies

Poly(esters) (PEs) derived from the reaction between bis(imido acids) containing Si as central atom and an aminoacidic residue, and a Si-containing diphenol, were synthesized according to the procedure described by Higashi. PEs were characterized by spectroscopic methods including 29Si NMR and the results were in agreement with the proposed structures. PEs were soluble in aprotic polar solvents and also in other common organic solvents such as tetrahydrofuran, acetone or CHCl3, which was attributed to the presence of aliphatic residues in the main chain provided by the amino acids, with the exception of those PEs which include p-aminobenzoic acid moieties. The PEs showed inherent viscosity values, indicative in some case of oligomeric species. Almost all the PEs showed good thermal stability, the most stable being those that include p-aminobenzoic acid as aminocidic residue due to the presence of a new p-aromatic ring in the main chain. Also it was possible to see that when the aromatic content was increased in the bis(imido acid) portion, the thermal decomposition temperature values also increased, especially when the values are compared with those PEs only with methyl groups bonded to the Si atoms. The Tg values were determined by DSC technique and those PEs with high aromatic content showed the highest Tg values due to the rigidity of the polymeric chain. On the other hand, when the size of the aliphatic side chains provided by the aminoacidic residues increased, the Tg values decreased due to the higher separation of the polymeric chains and consequently the higher free volume between them. The same tendency was observed as a function of the groups bonded to the Si atom of the bis(imido acids). PEs showed low UV–vis transparence due mainly to the high aromatic content, which favors the absorption.

Effect of side chain length and degree of polymerization on the decomposition and crystallization behaviour of chlorinated poly(vinyl ester) oligomers

Four members of a homologous series of chlorinated poly(vinyl ester) oligomers CCl3–(CH2CH (OCO(CH2)mCH3))n–Cl with degrees of polymerization of 10 and 20 were prepared by telomerisation using carbon tetrachloride. The number of side chain carbon atoms ranges from 2 (poly(vinyl acetate) to 18 (poly(vinyl stearate)). The effect of the n-alkyl side chain length and of the degree of polymerization on the thermal stability and crystallization behaviour of the synthesized compounds was investigated.All oligomers degrade in two major steps by first losing HCl and side chains with subsequent breakdown of the backbone. The members with short side chains, up to poly(vinyl octanoate), are amorphous and show internal plasticization, whereas those with high number of side chain carbon atoms are semi-crystalline due to side-chain crystallization. A better packing for poly(vinyl stearate) is also noticeable. The glass transition and melting temperatures as well as the onset temperature of decomposition are influenced to a larger extent by the side chain length than by the degree of polymerization. Thermal stability is improved if both the size and number of side chains increase, but only a long side chain causes a significant increase of the resistance to degradation. This results in a stabilization of PVAc so that oligomers from poly(vinyl octanoate) on are stable under atmospheric conditions. Thus, the way to design stable, chlorinated PVEs oligomers is to use a long n-alkyl side chain.

Responses of Glossina pallidipes and Glossina morsitans morsitans tsetse flies to analogues of δ-octalactone and selected blends

Previous studies have shown that δ-octalactone is an important component of the tsetse-refractory waterbuck (Kobus defassa) repellent odour blend. In the present study, structure-activity comparison was undertaken to determine the effects of the length of the side chain and ring size of the lactone on adult Glossina pallidipes and Glossina morsitans morsitans. The responses of the flies to each compound were studied in a two-choice wind tunnel. Increasing the chain length from C3 (δ-octalactone) to C4 (δ-nonalactone) enhanced repellency to both species (G. pallidipes from 60.0 to 72.0%, and G. m. morsitans from 61.3 to 72.6%), while increasing the ring size from six (δ-octalactone) to seven members (ε-nonalactone) changed the activity from repellency to attraction that was comparable to that of the phenolic blend associated with fermented cow urine (p>0.05). Blending δ-nonalactone with 4-methylguaiacol (known tsetse repellent) significantly (p<0.05) raised repellency to 86.7 and 91.7% against G. pallidipes and G. m. morsitans respectively. Follow-up Latin Square Designed field studies (Shimba hills in coastal areas in Kenya) with G. pallidipes populations confirmed the higher repellence of δ-nonalactone (with/without 4-methylguaiacol) compared to δ-octalactone (also, with/without 4-methylguaiacol). The results show that subtle structural changes of olfactory signals can significantly change their interactions with olfactory receptor neurons, and either shift their potency, or change their activity from repellence to attraction. Our results also lay down useful groundwork in the development of more effective control of tsetse by ‘push’, ‘pull’ and ‘push-pull’ tsetse control tactics.

Potent α-amino-β-lactam carbamic acid ester as NAAA inhibitors. Synthesis and structure–activity relationship (SAR) studies

4-Cyclohexylbutyl-N-[(S)-2-oxoazetidin-3-yl]carbamate (3b) is a potent, selective and systemically active inhibitor of intracellular NAAA activity, which produces profound anti-inflammatory effects in animal models. In the present work, we describe structure–activity relationship (SAR) studies on 3-aminoazetidin-2-one derivatives, which have led to the identification of 3b, and expand these studies to elucidate the principal structural and stereochemical features needed to achieve effective NAAA inhibition. Investigations on the influence of the substitution at the β-position of the 2-oxo-3-azetidinyl ring as well as on the effect of size and shape of the carbamic acid ester side chain led to the discovery of 3ak, a novel inhibitor of human NAAA that shows an improved physicochemical and drug-like profile relative to 3b. This favourable profile, along with the structural diversity of the carbamic acid chain of 3b, identify this compound as a promising new tool to investigate the potential of NAAA inhibitors as therapeutic agents for the treatment of pain and inflammation.

Zeolite-derived hybrid materials with adjustable organic pillars.

Porous organic-inorganic materials with tunable textural characteristics were synthesized using the top-down process by intercalating silsesquioxanes and polyhedral oligomeric siloxanes of different types between crystalline zeolite-derived layers. The influence of key parameters such as (i) linker nature (pure hydrocarbon, S-, N-containing); (ii) chain length in alkyl- and aryl bis(trialkoxysilyl) derivatives; (iii) denticity of the organic precursor molecules; (iv) nature and size of side chain in mono(trialkoxysilyl) substrates; (v) rigidity of the chain (saturated vs. unsaturated, aliphatic vs. aromatic); (vi) nature and size of leaving group on the structural and textural properties of formed hybrids was carefully addressed. It was established, that the optimal silsesquioxane appropriate for the formation of zeolite-derived hybrids with high textural characteristics should possess short alkyl or long aryl chains, relatively small leaving groups and denticity larger than 3. Addition of polydentate low-molecular binder improved the structural and textural characteristics of hybrids, especially when using bulky or hydrophilic linkers.

A Naturally Occurring Domestic Cat APOBEC3 Variant Confers Resistance to Feline Immunodeficiency Virus Infection

ABSTRACTApolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3; A3) DNA cytosine deaminases can be incorporated into progeny virions and inhibit lentiviral replication. On the other hand, viral infectivity factor (Vif) of lentiviruses antagonizes A3-mediated antiviral activities by degrading A3 proteins. It is known that domestic cat (Felis catus) APOBEC3Z3 (A3Z3), the ortholog of human APOBEC3H, potently suppresses the infectivity of vif-defective feline immunodeficiency virus (FIV). Although a recent report has shown that domestic cat encodes 7 haplotypes (hap I to hap VII) of A3Z3, the relevance of A3Z3 polymorphism in domestic cats with FIV Vif has not yet been addressed. In this study, we demonstrated that these feline A3Z3 variants suppress vif-defective FIV infectivity. We also revealed that codon 65 of feline A3Z3 is a positively selected site and that A3Z3 hap V is subject to positive selection during evolution. It is particularly noteworthy that feline A3Z3 hap V is resistant to FIV Vif-mediated degradation and still inhibits vif-proficient viral infection. Moreover, the side chain size, but not the hydrophobicity, of the amino acid at position 65 determines the resistance to FIV Vif-mediated degradation. Furthermore, phylogenetic analyses have led to the inference that feline A3Z3 hap V emerged approximately 60,000 years ago. Taken together, these findings suggest that feline A3Z3 hap V may have been selected for escape from an ancestral FIV. This is the first evidence for an evolutionary “arms race” between the domestic cat and its cognate lentivirus. IMPORTANCE Gene diversity and selective pressure are intriguing topics in the field of evolutionary biology. A direct interaction between a cellular protein and a viral protein can precipitate an evolutionary arms race between host and virus. One example is primate APOBEC3G, which potently restricts the replication of primate lentiviruses (e.g., human immunodeficiency virus type 1 [HIV-1] and simian immunodeficiency virus [SIV]) if its activity is not counteracted by the viral Vif protein. Here we investigate the ability of 7 naturally occurring variants of feline APOBEC3, APOBEC3Z3 (A3Z3), to inhibit FIV replication. Interestingly, one feline A3Z3 variant is dominant, restrictive, and naturally resistant to FIV Vif-mediated degradation. Phylogenetic analyses revealed that the ancestral change that generated this variant could have been caused by positive Darwinian selection, presumably due to an ancestral FIV infection. The experimental-phylogenetic investigation sheds light on the evolutionary history of the domestic cat, which was likely influenced by lentiviral infection.

Going Out on a Limb: Delineating The Effects of β-Branching, N-Methylation, and Side Chain Size on the Passive Permeability, Solubility, and Flexibility of Sanguinamide A Analogues.

It is well established that intramolecular hydrogen bonding and N-methylation play important roles in the passive permeability of cyclic peptides, but other structural features have been explored less intensively. Recent studies on the oral bioavailability of the cyclic heptapeptide sanguinamide A have raised the question of whether steric occlusion of polar groups via β-branching is an effective, yet untapped, tool in cyclic peptide permeability optimization. We report the structures of 17 sanguinamide A analogues designed to test the relative contributions of β-branching, N-methylation, and side chain size to passive membrane permeability and aqueous solubility. We demonstrate that β-branching has little effect on permeability compared to the effects of aliphatic carbon count and N-methylation of exposed NH groups. We highlight a new N-methylated analogue of sanguinamide A with a Leu substitution at position 2 that exhibits solvent-dependent flexibility and improved permeability over that of the natural product.