Correlation of the side-chain hubs with the functional residues in DNA binding protein structures

The structure networks of DNA-binding proteins have been constructed and analyzed. The detailed analysis of the networks indicates a strong relation between the positions of the residues interacting with DNA and those that form extensive interactions within the protein structure (called hubs). This study shows that the functional residues in these proteins are held in place by efficient scaffolding of the structure using side-chain interactions, thus highlighting the role of these side-chain hubs with respect to the functional residues in the protein structure.     

Ab initio study of the effect of side-chain reactions on the electronic structure of proteins

The effect of side-chain protonation and tautomerization of histidine on the electronic structure of proteins is investigated. Ab initio band structure results for protonated polyhistidine, polyhistidine in both tautomeric forms, polyglycine and polyalanine are reported. The density of states of the corresponding composite aperiodic polypeptides is studied using the simple negative factor counting method. It is shown how these side-chain reactions reduce the fundamental gap in aperiodic proteins, thereby modifying their conduction properties.     

The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins

The Raman optical activity (ROA) spectra of proteins show distinct patterns arising from the secondary structure. It is generally believed that the spectral contributions of the side-chains largely cancel out because of their flexibility and the occurrence of many side-chains with different conformations. Yet, the influence of the side-chains on the ROA patterns assigned to different secondary structures is unknown. Here, the first systematic study of the influence of all amino acid side-chains on the ROA patterns is presented based on density functional theory (DFT) calculations of an extensive collection of peptide models that include many different side-chain and secondary structure conformations. It was shown that the contributions of the side-chains to a large extent average out with conformational flexibility. However, specific side-chain conformations can have significant contributions to the ROA patterns. It was also shown that α-helical structure is very sensitive to both the exact backbone conformation and the side-chain conformation. Side-chains with χ₁≈−60° generate ROA patterns alike those in experiment. Aromatic side-chains strongly influence the amide III ROA patterns. Because of the huge structural sensitivity of ROA, the spectral patterns of proteins arise from extensive conformational averaging of both the backbone and the side-chains. The averaging results in the fine spectral details and relative intensity differences observed in experimental spectra.     

Differential ordering of the protein backbone and side chains during protein folding revealed by site-specific recombinant infrared probes

The time scale for ordering of the polypeptide backbone relative to the side chains is a critical issue in protein folding. The interplay between ordering of the backbone and ordering of the side chains is particularly important for the formation of β-sheet structures, as the polypeptide chain searches for the native stabilizing cross-strand interactions. We have studied these issues in the N-terminal domain of protein L9 (NTL9), a model protein with mixed α/β structure. We have developed a general approach for introducing site-specific IR probes for the side chains (azide) and backbone ((13)C═(18)O) using recombinant protein expression. Temperature-jump time-resolved IR spectroscopy combined with site-specific labeling enables independent measurement of the respective backbone and side-chain dynamics with single residue resolution. We have found that side-chain ordering in a key region of the β-sheet structure occurs on a slower time scale than ordering of the backbone during the folding of NTL9, likely as a result of the transient formation of non-native side-chain interactions.     

Total synthesis of a diastereomer of the marine natural product clavosolide A

The first total synthesis of the reported structure of the sponge metabolite clavosolide A is described using a Prins cyclisation to assemble the tetrahydropyran core followed by manipulation of the side-chain, dimerisation and finally glycosidation.     

DNA-templated polymerization of side-chain-functionalized peptide nucleic acid aldehydes

The DNA-templated polymerization of synthetic building blocks provides a potential route to the laboratory evolution of sequence-defined polymers with structures and properties not necessarily limited to those of natural biopolymers. We previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid (PNA) aldehydes. Here, we report the enzyme-free, DNA-templated polymerization of side-chain-functionalized PNA tetramer and pentamer aldehydes. We observed that polymerization of tetramer and pentamer PNA building blocks with a single lysine-based side chain at various positions in the building block could proceed efficiently and sequence specifically. In addition, DNA-templated polymerization also proceeded efficiently and in a sequence-specific manner with pentamer PNA aldehydes containing two or three lysine side chains in a single building block to generate more densely functionalized polymers. To further our understanding of side-chain compatibility and expand the capabilities of this system, we also examined the polymerization efficiencies of 20 pentamer building blocks each containing one of five different side-chain groups and four different side-chain regio- and stereochemistries. Polymerization reactions were efficient for all five different side-chain groups and for three of the four combinations of side-chain regio- and stereochemistries. Differences in the efficiency and initial rate of polymerization correlate with the apparent melting temperature of each building block, which is dependent on side-chain regio- and stereochemistry but relatively insensitive to side-chain structure among the substrates tested. Our findings represent a significant step toward the evolution of sequence-defined synthetic polymers and also demonstrate that enzyme-free nucleic acid-templated polymerization can occur efficiently using substrates with a wide range of side-chain structures, functionalization positions within each building block, and functionalization densities.     

Ferroelectric liquid crystal dopants with a chiral (R,R)-2,3-difluorooctyloxy side-chain: host dependence of the polarization power

The polarization powers δ_p of four chiral dopants with (R,R)-2,3-difluorooctyloxy side-chains were measured in four liquid crystal hosts with isotropic (I)-nematic (N)-smectic A (SmA)-smectic C (SmC) phase sequences. The four chiral dopants differ in terms of their core structures: 2-phenylpyridine (MDW950), biphenyl (5), 2-phenylpyrimidine (6) and 2-(3-nitrophenyl)pyrimidine (7). In each case, δ_p varies with the structure of the liquid crystal host, which is consistent with the behaviour of so-called Type II dopants that normally feature a chiral core structure. The δ_p(host) profile was found to depend on the degree of biaxiality of the dopant core structure, and on the degree of steric coupling between the chiral 2,3-difluorooctyloxy side-chain and the core. Conformational analyses at the B3LYP/6-31G* level suggest that the 2,3-difluorooctyloxy side-chain is conformationally more rigid than conventional chiral side-chains due to the added electrostatic repulsion of the two adjacent fluoro groups combined with the hyperconjugative 'gauche effect', and may therefore have a higher degree of biaxiality on the time average. This biaxial character should make the chiral side-chain more sensitive to variations in quadrupolar ordering imposed by the SmC phase of the liquid crystal host, and may therefore explain the dependence of δ_p on the host structure reported herein.     

Effect of side-chain disorder on the electronic structure of proteins

The influence of side-chain disorder on the electronic structure of proteins has been investigated in the case of polypeptides containing two or three different amino acid residues. It has been found that due to the different potentials of different side-chain groups, the original valence and conduction bands of the homopolypeptides are split into narrow bands. The comparison of the densities of electronic states in simple homopolypeptides and in composite polymers shows that new forbidden regions in the energy spectrum of proteins may develop. The consequences of these effects for the semiconductive properties of proteins are discussed.     

Direct observation of the main-chain conformation of a combined liquid-crystal polymer

The conformation of the main-chain (backbone) of a combined main-chain/side-chain liquid crystalline polymer has been qualitatively determined by small angle neutron scattering in the oriented nematic, the smectic A and the smectic C phases. The polymer backbone presents only a weak anisotropy, of prolate shape, in the nematic and the smectic C phases. A stronger reorientation of the backbones in the direction of the applied magnetic field is measured for the S_A phase. However, this anisotropy remains small compared to the stretching of a main-chain liquid crystal polymer and the smectic structure results apparently from side-chain ordering. On the other hand, hydrodynamic measurements show that the combined polymer, in solvent, is as flexible as a polystyrene chain. This result is compatible with an explanation for the weak observed anisotropy.     

A rational design for the directed helicity change of polyacetylene using dynamic rotaxane mobility by means of through-space chirality transfer

Directed helicity control of a polyacetylene dynamic helix was achieved by hybridization with a rotaxane skeleton placed on the side chain. Rotaxane-tethering phenylacetylene monomers were synthesized in good yields by the ester end-capping of pseudorotaxanes that consisted of optically active crown ethers and sec-ammonium salts with an ethynyl benzoic acid. The monomers were polymerized with [{RhCl(nbd)}(2)] (nbd=norbornadiene) to give the corresponding polyacetylenes in high yields. Polymers with optically active wheel components that are far from the main chain show no Cotton effect, thereby indicating the formation of racemic helices. Our proposal that N-acylative neutralization of the sec-ammonium moieties of the side-chain rotaxane moieties enables asymmetric induction of a one-handed helix as the wheel components approach the main chain is strongly supported by observation of the Cotton effect around the main-chain absorption region. A polyacetylene with a side-chain rotaxane that has a shorter axle component shows a Cotton effect despite the ammonium structure of the side-chain rotaxane moiety, thereby suggesting the importance of proximity between the wheel and the main chain for the formation of a one-handed helix. Through-space chirality induction in the present systems proved to be as powerful as through-bond chirality induction for formation of a one-handed helix, as demonstrated in an experiment using non-rotaxane-based polyacetylene that had an optically active binaphthyl group. The present protocol for controlling the helical structure of polyacetylene therefore provides the basis for the rational design of one-handed helical polyacetylenes.     

Structural correlations in comb heteropolymers in good and backbone-selective solvents

Molecular dynamics (MD) simulations of coarse-grained regular comb heteropolymers have been performed to explore structural correlations at equilibrium in a nonselective solvent and during the transition from coil to micelle in a backbone-selective solvent. We primarily consider the static structure factor measured directly from the simulations. In the good solvent, we consider cases ranging from short to long side chains, with respect to the spacer length. Reasonable agreement with a previously published theoretical structure factor is observed for a limited subset of the comb architectures in a small wavevector range. When the side chains are much longer than the spacers, the side-chain structure factor approaches that of starlike polymers. Additionally, plateau values of the structure factor scale with the side-chain length to the power of 0.736 when the side chains are shorter than the spacers. The transition from an open coil to a collapsed micelle is examined in MD simulations with explicit-solvent particles. Upon a sudden quench the from nonselective solvent to the backbone-selective solvent, the coil-to-micelle transition occurs via a side-chain clusterization mechanism. The time-dependent structure factors measured during the collapse process have plateau values that scale with the average cluster size to the power of 0.9. The origin of these two scaling exponents is still unknown. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 983-993, 2005     

A general strategy for the assignment of aliphatic side-chain resonances of uniformly 13C,15N-labeled large proteins

A general strategy is proposed to assign aliphatic side-chain resonances of large 13C,15N-labeled proteins without deuteration, using 4D 13C,15N-edited NOESY and MQ-(H)CCH-TOCSY experiments on the basis of prior assignments of backbone and 13Cbeta resonances. The strategy has been tested on a 214 residue protein (DdCAD-1) and applied to a chain-selectively 13C,15N-labeled hemoglobin (65 kDa). About 96 and 80% aliphatic side-chain spins in DdCAD-1 and hemoglobin have been assigned, respectively. The strategy proposed here will be very useful for the structure determination and dynamics characterization of large proteins by NMR.     

Recent Progress in the Construction of Natural De-O-Sulfonated Sulfonium Sugars with Antidiabetic Activities

A group of sulfonium salts equipped with a polyhydroxylated side-chain structure have been isolated and identified as potent α-glycosidase inhibitors. Consequently, they have become an attractive target in diverse research disciplines, including organic synthesis, drug discovery, and chemical biology. To this end, the development of practical and effective synthetic strategies, especially for more bioactive de-O-sulfonated sulfonium salts, is a significant research area in organic synthesis. An ideal synthetic methodology should provide easily accessible intermediates with high chemical stability for the key coupling reaction to diastereoselectively construct the sulfonium cation center. This minireview summarizes recently developed strategies applied in the construction of natural de-O-sulfonated sulfonium sugars: 1) acid-catalyzed de-O-sulfonation of sulfonium sulfate inner salts, 2) a coupling reaction between side-chain fragments containing leaving groups and a thiosugar, 3) a coupling reaction between side-chain fragments containing epoxide structures and a thiosugar, and 4) a two-step sequential S_N2 nucleophilic substitution between side-chain fragments containing thiol groups and a diiodide derivative.     

Exploring the active site of amine:pyruvate aminotransferase on the basis of the substrate structure-reactivity relationship: how the enzyme controls substrate specificity and stereoselectivity

An active site model of the amine:pyruvate aminotransferase (APA) from Vibrio fluvialis JS17 was constructed on the basis of the relationship between substrate structure and reactivity. Due to the broad substrate specificity of the APA, various amino donors (chiral and achiral amine, amino acid, and amino acid derivative) and amino acceptors (keto acid, keto ester, aldehyde, and ketone) were used to explore the active site structure. The result suggested a two-binding site model consisting of two pockets, one large (L) and the other small (S). The difference in the size of each binding pocket and strong repulsion for a carboxylate in the S pocket were key determinants to control its substrate specificity and stereoselectivity. The L pocket showed dual recognition mode for both hydrophobic and carboxyl groups as observed in the side-chain pockets of aspartate aminotransferase and aromatic aminotransferase. Comparison of the model with those of other aminotransferases revealed that the L and S pockets corresponded to carboxylate trap and side-chain pocket, respectively. The active site model successfully explains the observed substrate specificity as well as the stereoselectivity of the APA.     

Zur kenntnis der bitterstoffe aus cneoraceen-XVII

The isolation and structure elucidation of the protolimonoid $\text{1}$ with an unusual dioxiane side-chain is described.     

The fixed conformation of the leucyl side-chain in a tripeptide

The complete analysis of the ¹H NMR spectrum of the leucyl side-chain of a tripeptide allows the deduction of the conformation of this side-chain. In the peptide, in contrast to the free amino acid, the side-chain is in a single fixed conformation.     

Understanding the general packing rearrangements required for successful template based modeling of protein structure from a CASP experiment

As an alternative to the common template based protein structure prediction methods based on main-chain position, a novel side-chain centric approach has been developed. Together with a Bayesian loop modeling procedure and a combination scoring function, the Stone Soup algorithm was applied to the CASP9 set of template based modeling targets. Although the method did not generate as large of perturbations to the template structures as necessary, the analysis of the results gives unique insights into the differences in packing between the target structures and their templates. Considerable variation in packing is found between target and template structures even when the structures are close, and this variation is found due to 2 and 3 body packing interactions. Outside the inherent restrictions in packing representation of the PDB, the first steps in correctly defining those regions of variable packing have been mapped primarily to local interactions, as the packing at the secondary and tertiary structure are largely conserved. Of the scoring functions used, a loop scoring function based on water structure exhibited some promise for discrimination. These results present a clear structural path for further development of a side-chain centered approach to template based modeling.     

Three-dimensional packing structure and electronic properties of biaxially oriented poly(2,5-bis(3-alkylthiophene-2-yl)thieno[3,2-b]thiophene) films

We use a systematic approach that combines experimental X-ray diffraction (XRD) and computational modeling based on molecular mechanics and two-dimensional XRD simulations to develop a detailed model of the molecular-scale packing structure of poly(2,5-bis (3-tetradecylthiophene-2-yl)thieno[3,2-b]thiophene) (PBTTT-C(14)) films. Both uniaxially and biaxially aligned films are used in this comparison and lead to an improved understanding of the molecular-scale orientation and crystal structure. We then examine how individual polymer components (i.e., conjugated backbone and alkyl side chains) contribute to the complete diffraction pattern, and how modest changes to a particular component orientation (e.g., backbone or side-chain tilt) influence the diffraction pattern. The effects on the polymer crystal structure of varying the alkyl side-chain length from C(12) to C(14) and C(16) are also studied. The accurate determination of the three-dimensional polymer structure allows us to examine the PBTTT electronic band structure and intermolecular electronic couplings (transfer integrals) as a function of alkyl side-chain length. This combination of theoretical and experimental techniques proves to be an important tool to help establish the relationship between the structural and electronic properties of polymer thin films.     

蚕丝丝素纤维中氨基酸在丝素纤维的径向分布研究

通过显微镜观察、红外光谱、氨基酸组成分析、福林试剂分析等方法研究蚕丝丝素纤维的微结构、丝素表层和内层的结构差异 ,研究氨基酸尤其是对丝素纤维的结构和性能起重要影响的主要芳香族氨基酸———酪氨酸在丝素由表及里各层中的含量和分布 ,以期最终揭示丝素结构与蚕丝织物应用中的固有缺陷 (如泛黄、易皱、色牢度等 )的关系 .结果表明蚕丝丝素存在多层次结构 ,表层无定形区的比例较高 ,里层结晶区的比例较高 ;侧基较大的氨基酸和赖氨酸、组氨酸、胱氨酸、精氨酸、天门冬氨酸、苯丙氨酸、亮氨酸、谷氨酸、酪氨酸等在丝素的表层分布相对较多 ,而乙氨酸、丙氨酸、丝氨酸等小侧基氨基酸则在中间层至里层较多     

Discrimination of structural order and chromophore aggregation as factors effecting the photo-reorientation of azobenzene in copolyglutamate LB films

Photo-reorientation experiments have been performed on LB films of polyglutamates with azobenzene side chains and copolyglutamates with azobenzene moieties and non-photochromic mesogens as side chains. Incorporation of the non-photochromic phenylbenzoate and methyl-substituted biphenyl side chains prevents aggregation of the chromophores, but does not change the LB film structure. Photo-reorientation upon irradiation with polarized light is suppressed by the side-chain structure in the LB film, independent of chromophore aggregation. This structure is disrupted if the amount of side chains which can be photo-isomerized exceeds a critical number. After the structure has been disrupted, photo-reorientation is possible. Not only the chromophores, but also the non-photochromic side chains are reoriented in a cooperative manner.