Efficient side-chain and backbone assignment in large proteins: Application to tGCN5

In determining the structure of large proteins by NMR, it would be desirable to obtain complete backbone, side-chain, and NOE assignments efficiently, with a minimum number of experiments and samples. Although new strategies have made backbone assignment highly efficient, side-chain assignment has remained more difficult. Faced with the task of assigning side-chains in a protein with poor relaxation properties, the Tetrahymena histone acetyltransferase tGCN5, we have developed an assignment strategy that would provide complete side-chain assignments in cases where fast ¹³C transverse relaxation causes HCCH-TOCSY experiments to fail. Using the strategy presented here, the majority of aliphatic side-chain proton and carbon resonances can be efficiently obtained using optimized H(CC-CO)NH-TOCSY and (H)C(C-CO)NH-TOCSY experiments on a partially deuterated protein sample. Assignments can be completed readily using additional information from a ¹³ C-dispersed NOESY-HSQC spectrum. Combination of these experiments with H(CC)NH-TOCSY and (H)C(C)NH-TOCSY may provide complete backbone and side-chain assignments for large proteins using only one or two samples.     

Calculation of protein backbone geometry from alpha-carbon coordinates based on peptide-group dipole alignment.

An algorithm is proposed for the conversion of a virtual-bond polypeptide chain (connected C alpha atoms) to an all-atom backbone, based on determining the most extensive hydrogen-bond network between the peptide groups of the backbone, while maintaining all of the backbone atoms in energetically feasible conformations. Hydrogen bonding is represented by aligning the peptide-group dipoles. These peptide groups are not contiguous in the amino acid sequence. The first dipoles to be aligned are those that are both sufficiently close in space to be arranged in approximately linear arrays termed dipole paths. The criteria used in the construction of dipole paths are: to assure good alignment of the greatest possible number of dipoles that are close in space; to optimize the electrostatic interactions between the dipoles that belong to different paths close in space; and to avoid locally unfavorable amino acid residue conformations. The equations for dipole alignment are solved separately for each path, and then the remaining single dipoles are aligned optimally with the electrostatic field from the dipoles that belong to the dipole-path network. A least-squares minimizer is used to keep the geometry of the alpha-carbon trace of the resulting backbone close to that of the input virtual-bond chain. This procedure is sufficient to convert the virtual-bond chain to a real chain; in applications to real systems, however, the final structure is obtained by minimizing the total ECEPP/2 (empirical conformational energy program for peptides) energy of the system, starting from the geometry resulting from the solution of the alignment equations. When applied to model alpha-helical and beta-sheet structures, the algorithm, followed by the ECEPP/2 energy minimization, resulted in an energy and backbone geometry characteristic of these alpha-helical and beta-sheet structures. Application to the alpha-carbon trace of the backbone of the crystallographic 5PTI structure of bovine pancreatic trypsin inhibitor, followed by ECEPP/2 energy minimization with C alpha-distance constraints, led to a structure with almost as low energy and root mean square deviation as the ECEPP/2 geometry analog of 5PTI, the best agreement between the crystal and reconstructed backbone being observed for the residues involved in the dipole-path network.     

Proteins with simplified hydrophobic cores compared to other packing mutants

Efforts to design proteins with greatly reduced sequence diversity have often resulted in proteins with so-called molten globule properties. Substitutions were made at six neighboring sites in the major hydrophobic core of staphylococcal nuclease to create variants with all leucine, all isoleucine or all valine at these sites. The mutant proteins with simplified cores constructed here are quite unstable and have poorly packed cores, attested to by interaction energies. Eight related mutants with greater sequence diversity were also constructed. Comparison to these mutants and 159 other permutations of these 3 aliphatic side chains at these same 6 sites previously constructed shows that the simplified cores are not unusual in their stabilities or interaction energies. Further, crystal structures of the two mutants with the worst packing, as measured by interaction energies, showed no unusual disorder in the core. Therefore, reduction of sequence diversity is not necessarily incompatible with a single stable native structure. Other factors must also contribute to previous protein design failures.     

Assessing side-chain perturbations of the protein backbone: a knowledge-based classification of residue Ramachandran space

Grouping the 20 residues is a classic strategy to discover ordered patterns and insights about the fundamental nature of proteins, their structure, and how they fold. Usually, this categorization is based on the biophysical and/or structural properties of a residue's side-chain group. We extend this approach to understand the effects of side chains on backbone conformation and to perform a knowledge-based classification of amino acids by comparing their backbone phi, psi distributions in different types of secondary structure. At this finer, more specific resolution, torsion angle data are often sparse and discontinuous (especially for nonhelical classes) even though a comprehensive set of protein structures is used. To ensure the precision of Ramachandran plot comparisons, we applied a rigorous Bayesian density estimation method that produces continuous estimates of the backbone phi, psi distributions. Based on this statistical modeling, a robust hierarchical clustering was performed using a divergence score to measure the similarity between plots. There were seven general groups based on the clusters from the complete Ramachandran data: nonpolar/beta-branched (Ile and Val), AsX (Asn and Asp), long (Met, Gln, Arg, Glu, Lys, and Leu), aromatic (Phe, Tyr, His, and Cys), small (Ala and Ser), bulky (Thr and Trp), and, lastly, the singletons of Gly and Pro. At the level of secondary structure (helix, sheet, turn, and coil), these groups remain somewhat consistent, although there are a few significant variations. Besides the expected uniqueness of the Gly and Pro distributions, the nonpolar/beta-branched and AsX clusters were very consistent across all types of secondary structure. Effectively, this consistency across the secondary structure classes implies that side-chain steric effects strongly influence a residue's backbone torsion angle conformation. These results help to explain the plasticity of amino acid substitutions on protein structure and should help in protein design and structure evaluation.     

Addition of electrophilic lipids to actin alters filament structure

Pathophysiological processes associated with oxidative stress lead to the generation of reactive lipid species. Among them, lipids bearing unsaturated aldehyde or ketone moieties can form covalent adducts with cysteine residues and modulate protein function. Through proteomic techniques we have identified actin as a target for the addition of biotinylated analogs of the cyclopentenone prostaglandins 15-deoxy-Delta(12,14)-PGJ(2) (15d-PGJ(2)) and PGA(1) in NIH-3T3 fibroblasts. This modification could take place in vitro and mapped to the protein C-terminal end. Other electrophilic lipids, like the isoprostane 8-iso-PGA(1) and 4-hydroxy-2-nonenal, also bound to actin. The C-terminal region of actin is important for monomer-monomer interactions and polymerization. Electron microscopy showed that actin treated with 15d-PGJ(2) or 4-hydroxy-2-nonenal formed filaments which were less abundant and displayed shorter length and altered structure. Streptavidin-gold staining allowed mapping of biotinylated 15d-PGJ(2) at sites of filament disruption. These results shed light on the structural implications of actin modification by lipid electrophiles.     

Synthesis and antibacterial activity of novel ketolides with 11,12-quinoylalkyl side chains

A series of quinoylalkyl side chains was designed and synthesized, followed by introduction into ketolides by coupling with building block 6 or 32. The corresponding targets 7a–n, 33b, and 33e were tested for their in vitro activities against a series of macrolide-sensitive and macrolide-resistant pathogens. Some of them showed a similar antibacterial spectrum and comparable activity to telithromycin. Among them, two C2-F ketolides, compounds 33b and 33e, displayed excellent activities against macrolide-sensitive and macrolide-resistant pathogens.     

Characterization of advanced glycation end products: mass changes in correlation to side chain modifications

Advanced glycation end products (AGEs) that arise from the reaction of sugars with protein side chains are supposed to be involved in the pathogenesis of several diseases; therefore, the effects of AGEs on cells are the objective of numerous investigations. Because AGE modifications are an extremely heterogeneous group of side chain modifications, the exact characterization of an AGE-modified protein is impossible. To gain a deeper understanding about AGE formation kinetics and structures, AGEs can be characterized with respect to the degree of modification, specific side chain modifications, absorbance and fluorescence characteristics, and changes in the protein structure and molecular weight. For this study, human serum albumin (HSA)-AGEs derived from different concentrations of glucose, methyl glyoxal, and glyoxylic acid were used. The molecular mass of the obtained AGEs was determined using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The mass data were compared with earlier results concerning the degree of lysine and arginine side chain modifications and AGE-specific fluorescence and absorbance data. The molecular masses were found to gradually increase with increasing concentrations of the individual modifier without reaching a plateau. The mass increase correlates very well with the AGE-specific absorbance at 360 nm and with the degree of side chain modifications. The mass spectrometric data prove, for the first time, that an increasing absorbance at 360 nm is directly correlated to a mass increase during the AGE formation process.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Controlling the secondary-structure-forming tendencies of proteins by a backbone torsion-energy term

We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase or decrease the α-helix-forming-tendencies by lowering or raising the torsion-energy surface in the α-helix region and likewise increase or decrease the β-sheet-forming tendencies by lowering or raising the surface in the β-sheet region in the Ramachandran space. We applied this torsion-energy modification method to six force fields, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM27, OPLS-AA and OPLS-AA/L, and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides.     

'Molten-globule state': a compact form of globular proteins with mobile side-chains

In rat lacrimal glands, Forskolin induces a dose-dependent [³H]protein release. This effect can be potentiated by papaverine. As for the other inducers whose effects on protein secretion are assumed to be cAMP-mediated, Forskolin secretion time course shows a latency. Isoproterenol decreases the Forskolin EC_5- at least 60--times. On the other hand, Forskolin enhances the efficacy of isoproterenol without affecting its potency. As a whole, the data collected show that isoproterenol-induced [³H]protein secretion in rat lacrimal glands involved adenylate cyclase activation by coupling with β-adrenergic receptors.     

1H, 13C and 15N backbone and side chain resonance assignments of a Myxococcus xanthus anti-repressor with no known sequence homologues

The CarS antirepressor activates a photo-inducible promoter in Myxococcus xanthus by physically interacting with the CarA repressor and eliminating the latter’s binding to operator DNA. Interestingly, interactions with both CarS and operator are crucially dependent on the DNA recognition helix of the CarA winged-helix DNA-binding domain. The CarA–CarS and the CarA-operator interfaces therefore overlap, and CarS may have structural features that mimic operator DNA. CarS has no known sequence homologues and its Gly and Pro contents are unusually high. Here, we report ¹H, ¹³C and ¹⁵N backbone and side chain assignments of CarS1, an 86-residue truncated yet fully functional variant of CarS. Secondary structural elements inferred from these data differ from those predicted from sequence.     

Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: development of strategies and construction of models for myoglobin, lysozyme, and thymosin beta 4.

Recently we developed methods for the construction of knowledge-based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three-dimensional models of polypeptide chains. The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model. The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X-ray analysis and thymosin beta 4, a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.     

Temperature-dependent spectral density analysis applied to monitoring backbone dynamics of major urinary protein-I complexed with the pheromone 2-sec-butyl-4,5-dihydrothiazole*

Backbone dynamics of mouse major urinary protein I (MUP-I) was studied by (15)N NMR relaxation. Data were collected at multiple temperatures for a complex of MUP-I with its natural pheromonal ligand, 2- sec -4,5-dihydrothiazole, and for the free protein. The measured relaxation rates were analyzed using the reduced spectral density mapping. Graphical analysis of the spectral density values provided an unbiased qualitative picture of the internal motions. Varying temperature greatly increased the range of analyzed spectral density values and therefore improved reliability of the analysis. Quantitative parameters describing the dynamics on picosecond to nanosecond time scale were obtained using a novel method of simultaneous data fitting at multiple temperatures. Both methods showed that the backbone flexibility on the fast time scale is slightly increased upon pheromone binding, in accordance with the previously reported results. Zero-frequency spectral density values revealed conformational changes on the microsecond to millisecond time scale. Measurements at different temperatures allowed to monitor temperature dependence of the motional parameters.     

酸与酸肥混合处理对瑞典中部里兹堡松林地上部分的影响

在实验处理期间,瑞典Ｌｉｓｅｌｂｏ地区实验松林受益于硫酸的施用和酸肥的混合使用．１９７１～１９７７年间,酸处理的松树林分基径面积的增长比对照提高了４％;１９７６年酸处理结束,但其潜在的正效应在１９７８～１９８５年间得到增强,基径面积的增长比对照提高了２０％,随后的某一阶段开始下降,１９９３～１９９４为１１％．酸肥混合处理的松树林分的基径面积增长在１９７１～１９７７年比对照提高了３８％;１９７８～１９８５年略有下降,为３０％;１９９３～１９９４年间为－１６％,提示酸肥混合处理对松林基径面积的促进作用至少在１９８５年处理结束后开始减弱,最后表现为负的生长效应．１９９４年,和对照、酸处理的松林样地比,酸肥处理的松林地上部分具有较高的生物现存量,较低的针叶生产力水平．然而,酸处理的松林样地的地上部分现存量相对高于对照,明显低于酸肥混合处理,其针叶生产力水平则相对比对照的高,显著高于酸肥混合处理的松林样地     

The binding of analogs of porphyrins and chlorins with elongated side chains to albumin

In previous studies, we demonstrated that elongation of side chains of several sensitizers endowed them with higher affinity for artificial and natural membranes and caused their deeper localization in membranes. In the present study, we employed eight hematoporphyrin and protoporphyrin analogs and four groups containing three chlorin analogs each, all synthesized with variable numbers of methylenes in their alkyl carboxylic chains. We show that these tetrapyrroles’ affinity for bovine serum albumin (BSA) and their localization in the binding site are also modulated by chain lengths. The binding constants of the hematoporphyrins and protoporphyrins to BSA increased as the number of methylenes was increased. The binding of the chlorins depended on the substitution at the meso position opposite to the chains. The quenching of the sensitizers’ florescence by external iodide ions decreased as the side chains became longer, indicating to deeper insertion of the molecules into the BSA binding pocket. To corroborate this conclusion, we studied the efficiency of photodamage caused to tryptophan in BSA upon illumination of the bound sensitizers. The efficiency was found to depend on the side-chain lengths of the photosensitizer. We conclude that the protein site that hosts these sensitizers accommodates different analogs at positions that differ slightly from each other. These differences are manifested in the ease of access of iodide from the external aqueous phase, and in the proximity of the photosensitizers to the tryptophan. In the course of this study, we developed the kinetic equations that have to be employed when the sensitizer itself is being destroyed.     

A novel synthetic approach to (20R)- and (20S)-21-hydroxy steroids. Synthesis of a marine sterol 21-hydroxycholesterol

A short and efficient synthesis of steroid synthons, di(tert-butyldimethylsilyl) ethers of 3,21-dihydroxy-24-nor-chol-5-en-23-al (8 and 10) and of ethyl 3,21-dihydroxy-25-homo-chola-5,23-dien-25-oate (9 and 11), having natural (20R) and unnatural (20S) configuration from 3β-(tert-butyldimethylsilyloxy)-14α,20ξ-card-5-enolide (2) is reported. Further elongation of the side chain of these synthons provides a new method for the synthesis of (20R) and (20S)-21-hydroxy steroids. The utility of the method was exemplified by the synthesis of a natural marine sterol - 21-hydroxycholesterol (18).     

Practical tools for molecular modeling of complex carbohydrates and their interactions with proteins

Computer modeling has become a valuable component of studies of carbohydrate three-dimensional structures and their relationship to function and properties. In this paper we examine the methods required for conformational modeling of carbohydrates, and we present a series of tools that have been developed to this end. These tools can be integrated into three-dimensional real-time molecular modeling software. A data base of pre-optimized carbohydrate fragments has been established to be used further in the construction of much more complex molecules. In addition we describe some possible uses of a data base of three dimensional structures of the disaccharide fragments present in the glycan moiety ofN-glycoprotein. A molecular mechanical force field appropriate for the conformational analysis of oligosaccharides has been derived by the addition of new parameters to the Tripos force field and is compatible with protein simulations. The new parametrization has been assessed in three stages of increasing complexity: computations of potential energy surfaces, conformational refinement of relevant oligosaccharides, modeling at the atomic level of a protein/carbohydrate complex.     

An effective synthesis of an arabinogalactan with a beta-(1-->6)-linked galactopyranose backbone and alpha-(1-->2) arabinofuranose side chains

An octasaccharide, beta-D-Galp-(1-->6)-[alpha-L-Araf-(1-->2)]-beta-D-Galp-(1-->6)-beta-D-Galp-(1-->6)-[alpha-L-Araf-(1-->5)-alpha-L-Araf-(1-->2)]-beta-D-Galp-(1-->6)-beta-D-Galp-1-->OMP was synthesized. 4-methoxyphenyl 2,3,4-tri-O-benzoyl-beta-D-galactopyranoside (5), 2,6-di-O-acetyl-3,4-di-O-benzoyl-alpha-D-galactopyranosyl trichloroacetimidate (9), and 4-methoxyphenyl 2-O-acetyl-3,4-di-O-benzoyl-beta-D-galactopyranoside (11), 2,3,4,6-tetra-O-benzoyl-alpha-D-galactopyranosyl trichloroacetimidate (12), and 2,3,5-tri-O-benzoyl-alpha-L-arabinofuranosyl trichloroacetimidate (17) were used as the synthons. A concise route was used to gain the tetrasaccharide donor 19 by the use of 11, 12, 5, and 17. Meanwhile, treatment of 5 with 9 yielded beta-(1-->6)-linked disaccharide 20, and subsequent selective 6-O-deacetylation produced the disaccharide acceptor 21. Reaction of 21 with 19 gave 22, and subsequent selective 2-O-deacetylation afforded the hexasaccharide acceptor 23. Condensation of 23 with alpha-L-(1-->5)-linked arabinofuranose disaccharide 24, followed by deprotection, yielded the target octasaccharide.     

Kinetic studies of folding of the B-domain of staphylococcal protein A with molecular dynamics and a united-residue (UNRES) model of polypeptide chains

Langevin dynamics is used with our physics-based united-residue (UNRES) force field to study the folding pathways of the B-domain of staphylococcal protein A (1BDD (alpha; 46 residues)). With 400 trajectories of protein A started from the extended state (to gather meaningful statistics), and simulated for more than 35 ns each, 380 of them folded to the native structure. The simulations were carried out at the optimal folding temperature of protein A with this force field. To the best of our knowledge, this is the first simulation study of protein-folding kinetics with a physics-based force field in which reliable statistics can be gathered. In all the simulations, the C-terminal alpha-helix forms first. The ensemble of the native basin has an average RMSD value of 4 A from the native structure. There is a stable intermediate along the folding pathway, in which the N-terminal alpha-helix is unfolded; this intermediate appears on the way to the native structure in less than one-fourth of the folding pathways, while the remaining ones proceed directly to the native state. Non-native structures persist until the end of the simulations, but the native-like structures dominate. To express the kinetics of protein A folding quantitatively, two observables were used: (i) the average alpha-helix content (averaged over all trajectories within a given time window); and (ii) the fraction of conformations (averaged over all trajectories within a given time window) with Calpha RMSD values from the native structure less than 5 A (fraction of completely folded structures). The alpha-helix content grows quickly with time, and its variation fits well to a single-exponential term, suggesting fast two-state kinetics. On the other hand, the fraction of folded structures changes more slowly with time and fits to a sum of two exponentials, in agreement with the appearance of the intermediate, found when analyzing the folding pathways. This observation demonstrates that different qualitative and quantitative conclusions about folding kinetics can be drawn depending on which observable is monitored.