Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.     

Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification

Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.     

Cα-Cβ chromophore bond dissociation in protonated tyrosine-methionine, methionine-tyrosine, tryptophan-methionine, methionine-tryptophan and their sulfoxide analogs

C(α)-C(β) chromophore bond dissociation in some selected methionine-containing dipeptides induced by UV photons is investigated. In methionine containing dipeptides with tryptophan as the UV chromophore, the tryptophan side chain is ejected either as an ion or as a neutral fragment while in dipeptides with tyrosine, the tyrosine side chain is lost only as a neutral fragment. Mechanisms responsible for these fragmentations are proposed based on measured branching ratios and fragmentation times, and on the results of DFT/B3-LYP calculations. It appears that the C(α)-C(β) bond cleavage is a non-statistical dissociation for the peptides containing tyrosine, and occurs after internal conversion for those with tryptophan. The proposed mechanisms are governed by the ionization potential of the aromatic side chain compared to that of the rest of the molecule, and by the proton affinity of the aromatic side chain compared to that of the methionine side chain. In tyrosine-containing peptides, the presence of oxygen on sulfur of methionine presumably reduces the ionization potential of the peptide backbone, facilitating the loss of the side chain as a neutral fragment. In tryptophan-containing peptides, the presence of oxygen on methionyl-sulfur expedites the transfer of the proton from the side chain to the sulfoxide, which facilitates the loss of the neutral side chain.     

An NMR study of mobility in a crystalline side‐chain comblike polymer

Carbon‐13 spin–lattice relaxation times are measured for poly(octadecyl acrylate) above and below the melting point of the crystalline side chains. The chain backbone has long spin–lattice relaxation times below the melting point that shorten by more than an order of magnitude as the melting point range is traversed. Below the melting point, the backbone is nearly immobilized with spin–lattice relaxation changing very slowly with temperature. Above the melting point, the shorter spin–lattice relaxation times are typical of a rubber above the glass transition and decrease with increasing temperature. The methylene groups in the side chain are quite mobile well below the melting point, indicating fairly rapid anisotropic motion within the crystal. The methyl group at the end of the chain and the adjacent methylene group have longer spin–lattice relaxation times, indicating the greatest side‐chain mobility at the end, which is in the middle of the crystal structure. The side‐chain carbon adjacent to the carbonyl group is as mobile as the majority of the side‐chain carbon, indicating side‐chain mobility extends to all of the side‐chain CH₂ groups. The abrupt transition in the mobility of the backbone is not typical of the amorphous phase in a semicrystalline polymer where the backbone units can crystallize. The close proximity of every backbone segment to the crystalline domain locks backbone segmental motion below the melting point. Melting and crystallization of the side chains switch segmental motion of the backbone on and off. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 1548–1552, 2001     

Highly stereoselective peptide modifications through Pd-catalyzed allylic alkylations of chelated peptide enolates

Deprotonation of peptides in the presence of zinc chloride gives rise to highly reactive nucleophiles that can be subjected to palladium-catalyzed allylic alkylation reactions. Excellent diastereoselectivities are obtained that are nearly independent of the allylic substrate used. By using this protocol, highly functionalized side chains can also be incorporated in excellent yields and selectivities. The stereochemical outcome of the reaction is exclusively controlled by the peptide chain as long as terminal pi-allyl-palladium complexes are involved. Probably, there is a threefold coordination, at least, of the deprotonated peptide chain to the chelating zinc ion. In such metal peptide complexes, one face of the generated enolate is shielded by the side chain of the adjacent amino acid, thus directing the electrophilic attack onto the opposite face. This behavior explains why an S amino acid always generates an R amino acid (and the other way round).     

Stoichiometric polyelectrolyte complexes as comb copolymers

The collapse behavior of a single comblike copolymer chain has been studied by Monte Carlo simulations. It has been supposed that the solvent is good for the side chains but the solvent quality for the backbone chain changes. It has been shown that depending on the structural parameters of the comb copolymer (the lengths of the backbone and side chains, grafting density of the side chains) various thermodynamically stable morphologies of the collapsed backbone chain can be realized. In addition to ordinary spherical globule we have observed elongated structures as well as necklace-like conformations. The proposed model can be used to describe conformational behavior of stoichiometric complexes between block copolymers with a polyelectrolyte short block and oppositely charged linear homopolymers.     

N-烷基化聚对苯二甲酰对苯二胺梳状高分子中烷基侧链对刚性主链堆积行为的影响

基于聚对苯二甲酰对苯二胺(PPTA), 采用N-烷基化方法制备了系列PPTACns(烷基侧链碳原子数n=8, 10, 12, 14, 16, 18)刚性主链梳状高分子, 利用DSC, XRD和FTIR等方法研究了其主链堆积行为、 分子链构象及热性能等与烷基侧链长度及结晶特性之间的关系. XRD和DSC结果表明, 当烷基侧链碳原子数达到14时, 烷基侧链发生结晶. XRD结果显示, PPTACns具有层状结构, 烷基侧链长度对主链层间距影响显著. FTIR研究发现, 烷基侧链的聚集状态对PPTACns分子链的构象产生较大影响, 伴随着烷基侧链结晶的熔融, PPTACns的分子链构象发生显著改变. 烷基侧链处于熔融状态的PPTACns的ν_C=O和γ_C-H谱带峰位与烷基侧链不结晶的PPTACn接近.     

Backbone effects on the anchoring of side-chain polymer liquid crystals

By comparing the anchoring behaviour of (end-on) side chain polymer liquid crystals with that of the corresponding low molecular mass liquid crystals, we have studied the effect of the backbone on the anchoring of side chain polymer liquid crystals. We can distinguish two different effects: the loss of rotational freedom of the side groups and the interaction of the polymer chain with the surface. In the case of free surfaces, we can formulate a general rule stating that compounds with side groups ending with an aliphatic chain (at least four carbon atoms long) exhibit a homeotropic anchoring, and compounds with side groups ending with a polar group exhibit a planar anchoring.     

On the shape of bottle-brush macromolecules: systematic variation of architectural parameters

We measured the form factor of bottle-brush macromolecules under good solvent conditions with small-angle neutron scattering and static light scattering. The systems under investigation are brushes, synthesized via the grafting-from route, built from a poly(alkyl methacrylate) backbone to which poly(n-butyl acrylate) side chains are densely grafted. The aim of our work is to study how the systematic variation of structural parameters such as the side chain length and backbone length change the conformation of the polymer brushes in solution. All spectra can be consistently described by a model, considering the bottle-brush polymers as flexible rods with internal density fluctuations. Parameters discussed are (1) the contour length per main chain monomer l(b), (2) the fractal dimension of the side chains Ds, as well as (3) the fractal dimension D, and (4) the Kuhn length lambdak of the overall brush. l(b)=0.253+/-0.008 nm is found to be independent of the side chain length and equal to the value found for the bare main chain, indicating a strongly stretched conformation for the backbone due to the presence of the side chains. The fractal dimension of the side chains is determined to be Ds=1.75+/-0.07 which is very close to the value of 10.588 approximately 1.70 expected for a three-dimensional self-avoiding random walk (3D-SAW) under good solvent conditions. On larger length scales the overall brush appears to be a 3D-SAW itself (D=1.64+/-0.08) with a Kuhn-step length of lambdak=70+/-4 nm. The value is independent of the side chain length and 46 times larger than the Kuhn length of the bare backbone (lambdak=1.8+/-0.2 nm). The ratio of Kuhn length to brush diameter lambda(k)d>or=20 determines whether lyotropic behavior can be expected or not. Since longer side chains do not lead to more persistent structures, lambda(k)d decreases from 8 to 4 with increasing side chain length and lyotropic behavior becomes unlikely.     

Incorporation of a conjugated side‐chain in regioregular polythiophenes: Chiroptical properties and selective oxidation

The synthesis, aggregation, and optical properties of a chiral, regioregular polythiophene, substituted with a conjugated substituent, are described. The polymer was prepared using a Stille coupling reaction. The fact that the side‐chain contributes to the absorption (UV‐vis), emission (fluorescence), and redox behavior (cyclic voltammetry) of the material demonstrates that the substituent contributes to the electronic properties. It was shown that the conjugated side‐chain chirally stacks in conditions in which the polymer backbone aggregates, which demonstrates the ability of conjugated polymers to induce a (chiral) lamellar organization of conjugated moieties, present in their side‐chain. The aggregation of both the side‐chain and the backbone was monitored using UV‐vis and CD spectroscopy. Finally, it is shown that the conjugated side‐chain can selectively be oxidized, without oxidizing the polythiophene backbone. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 1891–1900, 2009     

Structural and energetic effects in the molecular recognition of protonated peptidomimetic bases by 18-crown-6

Absolute 18-crown-6 (18C6) affinities of nine protonated peptidomimetic bases are determined using guided ion beam tandem mass spectrometry techniques. The bases (B) included in this work are mimics for the n-terminal amino group and the side chains of the basic amino acids, i.e., the favorable sites for binding of 18C6 to peptides and proteins. Isopropylamine is chosen as a mimic for the n-terminal amino group, imidazole and 4-methylimidazole are chosen as mimics for the side chain of histidine (His), 1-methylguanidine is chosen as a mimic for the side chain of arginine (Arg), and several primary amines including methylamine, ethylamine, n-propylamine, n-butylamine, and 1,5-diamino pentane as mimics for the side chain of lysine (Lys). Theoretical electronic structure calculations are performed to determine stable geometries and energetics for neutral and protonated 18C6 and the peptidomimetic bases, as well as the proton bound complexes comprised of these species, (B)H(+)(18C6). The measured 18C6 binding affinities of the Lys side chain mimics are larger than the measured binding affinities of the mimics for Arg and His. These results suggest that the Lys side chains should be the preferred binding sites for 18C6 complexation to peptides and proteins. Present results also suggest that competition between Arg or His and Lys for 18C6 is not significant. The mimic for the n-terminal amino group exhibits a measured binding affinity for 18C6 that is similar to or greater than that of the Lys side chain mimics. However, theory suggests that binding to n-terminal amino group mimic is weaker than that to all of the Lys mimics. These results suggest that the n-terminal amino group may compete with the Lys side chains for 18C6 complexation.     

Solvent‐Induced Length Variation of Cylindrical Brushes

Polymacromonomers with a main chain much larger than the side‐chain length adopt the form of cylindrical brush polymers the contour length per main‐chain monomer of which depends on the side‐chain length. In the present investigation it is demonstrated that the length per monomer also depends on the solvent quality, i.e., the cylinders are shorter in a poor solvent as compared to a good solvent. It is argued that the repulsion of the side chains represents the extension force, which acts against the entropic contraction force of the main chain. Thus, cylindrical brushes may be suitable as responsive materials for sensors, actuators or soft machines.     

Influence of Side Chain Conformation on the Activity of Glycosidase Inhibitors

Substrate side chain conformation impacts reactivity during glycosylation and glycoside hydrolysis and is restricted by many glycosidases and glycosyltransferases during catalysis. We show that the side chains of gluco and manno iminosugars can be restricted to predominant conformations by strategic installation of a methyl group. Glycosidase inhibition studies reveal that iminosugars with the gauche,gauche side chain conformations are 6- to 10-fold more potent than isosteric compounds with the gauche,trans conformation; a manno-configured iminosugar with the gauche,gauche conformation is a 27-fold better inhibitor than 1-deoxymannojirimycin. The results are discussed in terms of the energetic benefits of preorganization, particularly when in synergy with favorable hydrophobic interactions. The demonstration that inhibitor side chain preorganization can favorably impact glycosidase inhibition paves the way for improved inhibitor design through conformational preorganization.     

Open science grid study of the coupling between conformation and water content in the interior of a protein

Computational grids are a promising resource for modeling complex biochemical processes such as protein folding, penetration of gases or water into proteins, or protein structural rearrangements coupled to ligand binding. We have enabled the molecular dynamics program CHARMM to run on the Open Science Grid. The implementation is general, flexible, easily modifiable for use with other molecular dynamics programs and other grids and automated in terms of job submission, monitoring, and resubmission. The usefulness of grid computing was demonstrated through the study of hydration of the Glu-66 side chain in the interior of protein staphylococcal nuclease. Multiple simulations started with and without two internal water molecules shown crystallographically to be associated with the side chain of Glu-66 yielded two distinct populations of rotameric states of Glu-66 that differed by as much as 20%. This illustrates how internal water molecules can bias protein conformations. Furthermore, there appeared to be a temporal correlation between dehydration of the side chain and conformational transitions of Glu-66. This example demonstrated how difficult it is to get convergence even in the relatively simple case of a side chain oscillating between two conformations. With grid computing, we also benchmarked the self-guided Langevin dynamics method against the Langevin dynamics method traditionally used for temperature control in molecular dynamics simulations and showed that the two methods yield comparable results.     

Combined main chain/side chain polymers. A new class of liquid crystalline polymers with unusual structural, thermodynamic and dynamic properties

Combined main chain/side chain polymers carry rigid rod-like mesogenic units both in the side chain and along the chain backbone. The properties of such combined systems are expected to be controlled by the competition of the interactions between the mesogenic units in the side and main chains as well as the tendency of the chain backbones to maximize their entropy. The thermodynamic, structural and dynamic properties of such combined main chain/side chain liquid-crystalline polymers were investigated for various chain architectures. The combined systems were found to display properties corresponding in many cases to a favourable superposition of properties characteristic of both main and side chain systems. These include high transition temperatures (up to 530 K) and broad ranges of stability of liquid-crystalline phases (up to about ΔT = 170 K). The orientational order parameter was found to approach values of 0.9 and it was possible to orient some of the polymers in weak external fields such as 1 T for instance, for magnetic fields. Smectic antiphase formation corresponding to that observed in low molar mass systems carrying strong longitudinal dipoles and resulting from the presence of incommensurable lengths were observed in those cases in which the side groups were attached directly to the rigid part of the chain backbone whereas no such effects occurred if the side groups were fixed to the flexible part of the main chain. The reorientational motion of the mesogens about their short axis, which couples to dielectric and electro-optical properties was found to have a surprisingly low activation energy (as low as 115 kJ/mol) and a strong anisotropy of the dielectric constant (Δε = 7) despite a relatively small concentration of dipoles. It thus seems that the combined systems may be the material of choice for many future applications.     

The effect of histidine oxidation on the dissociation patterns of peptide ions

Oxidative modifications to amino acid side chains can change the dissociation pathways of peptide ions, although these variations are most commonly observed when cysteine and methionine residues are oxidized. In this work we describe the very noticeable effect that oxidation of histidine residues can have on the dissociation patterns of peptide ions containing this residue. A common product ion spectral feature of doubly charged tryptic peptides is enhanced cleavage at the C-terminal side of histidine residues. This preferential cleavage arises as a result of the unique acid/base character of the imidazole side chain that initiates cleavage of a proximal peptide bond for ions in which the number of protons does not exceed the number of basic residues. We demonstrate here that this enhanced cleavage is eliminated when histidine is oxidized to 2-oxo-histidine because the proton affinity and nucleophilicity of the imidazole side chain are lowered. Furthermore, we find that oxidation of histidine to 2-oxo-histidine can cause the misassignment of oxidized residues when more than one oxidized isomer is simultaneously subjected to tandem mass spectrometry (MS/MS). These spectral misinterpretations can usually be avoided by using multiple stages of MS/MS (MS(n)) or by specially optimized liquid chromatographic separation conditions. When these approaches are not accessible or do not work, N-terminal derivatization with sulfobenzoic acid avoids the problem of mistakenly assigning oxidized residues.     

Thermolysis of Neopentylcobalamin Analogs Complexed to Haptocorrin: Side Chain Entropy and Activation of Organocobalamins for Carbon-Cobalt Bond Homolysis

The kinetics of the thermal Co-C bond homolysis of the complexes of a vitamin B(12) binding protein (haptocorrin) with a series of analogs of neopentylcobalamin modified in side chain structure have been studied. The analogs include the C13 epimer in which the e propionamide side chain adopts an "upwardly" axial conformation and a series of c side chain-modified analogs, including the c-monocarboxylate, the c-N-methylamide, the c-N,N-dimethylamide, and the c-N-isopropylamide. Activation parameters for the thermal homolysis of these complexes show that the previously observed stabilization of alkylcobalamins by haptocorrin is due to both enthalpic and entropic factors. With the exception of that for the analog having the bulkiest c side chain substituent, neopentylcobalamin-c-N-isopropylamide, the enthalpies of activation are independent of analog structure, but the entropies of activation increase with the steric bulk of the c side chain and with the number of "upwardly" projecting side chains, as previously observed for protein-free neopentylcobalamin and its analogs. The results are discussed in terms of the solvent cage effect on Co-C bond homolysis and the importance of corrin ring side chain thermal motions to the entropy of activation for this reaction.     

Well-packed chains and aggregates in the emission mechanism of conjugated polymers

We synthesized dialkoxy-substituted poly[phenylene vinylene]s (dROPPV-1/1, 0.2/1, and 0/1) consisting of two repeating units with different side-chain lengths (methoxy and 3,7-dimethyloctyloxy). These polymers can serve as a model system to clarify roles of aggregates (the sites with ground-state interchain interactions) and the independent chain segments in the well-packed chains (the chain segments that are compactly packed without interaction) in the emission mechanism of conjugated polymers. Due to the packing of polymer chains, films of all of these polymers are accessible to interchain excitations, after which excitons can re-form to result in delayed luminescence. Besides, some chains form aggregates so that the delayed luminescence is no more the ordinary single-chain emission but red-shifted and less structured. Not only the re-formation of these indirect excitons but also the aggregation of chains are facilitated in the polymers with short methoxy side groups, revealing that both packing and aggregation of chain segments require a short spacing between polymer chains. However, the incorporation of other side chains such as the 3,7-dimethyloctyloxy group to dROPPVs is necessary for the formation of aggregates because these long branched side chains can reduce the intrachain order imposed by the short methoxy groups, which accounts for the absence of aggregate emission in the well-studied poly[2,5-dimethoxy-1,4-phenylene vinylene]. This study reveals that the well-packed chains do not necessarily form aggregates. We also show that the photophysical properties and the film morphology of conjugated polymers can be deliberately controlled by fine-tuning of the copolymer compositions, without altering the optical properties of single polymer chains (e.g., as in dilute solutions).     

Conformations in dioctyl substituted polyfluorene: a combined theoretical and experimental Raman scattering study

The structural properties of polyfluorenes (PF) are extremely sensitive to the choice of functionalizing side chains. Dioctyl substituted PF (PF8) adopts metastable structures that depend upon the thermal history and choice of solvents used in film forming conditions. We present a detailed study of the changes in the backbone and side chain morphology in PF8, induced by the various crystallographic phases, using Raman scattering techniques. The vibrational frequencies and intensities of fluorene oligomers are calculated using hybrid density-functional theory with a 3-21G(*) basis set. The alkyl side chains are modeled as limiting conformations: all anti, anti-gauche-gauche, and end gauche representations. The calculated vibrational spectra of single chain oligomers in conjunction with our experimental results demonstrate the beta phase, which is known to originate in regions of enhanced chain planarity as a direct consequence of the alkyl side chain conformation.     

Pharmacologically interesting compounds—I: High resolution mass spectra of phenothiazines

The mass spectra of twenty-six commercially available medicinal phenothiazines have been determined at high resolution. In each compound, the side chain attached to the 10-position of the phenothiazine ring contains nitrogen and fission of the C? C bond α to this nitrogen gives in most cases the base peak. Some of the compounds are also substituted at the 2-position and this substituent generally remains intact, though some substituents such as acetyl, propionyl, methoxyl and methylthio can undergo fragmentation. Fragmentations fall into three groups; those which give ions representing a part of the side chain; those which give ions representing the intact phenothiazine ring with part of the side chain attached; those which give ions representing a partially fragmented ring system.