1.2A分辨率胰岛素二体中两个分子间的构象差异

以1.2A分辨率的胰岛素精细结构模型为基础,分析并确定了三方二锌猪胰岛素晶体中二体分子的构象差异。构象差异不仅表现于侧链残基,也涉及到主链构象的变化。二体分子的构象差异带来的不对称性也明显地表现在二体分子的氢键体系和结合水的差异。局部微环境的不同是维持二体分子构象差异的稳定因素。文中对有重要差异的残基作了较详细的分析和讨论。     

Positive contribution of hydration structure on the surface of human lysozyme to the conformational stability

Water molecules make a hydration structure with the network of hydrogen bonds, covering on the surface of proteins. To quantitatively estimate the contribution of the hydration structure to protein stability, a series of hydrophilic mutant human lysozymes (Val to Ser, Tyr, Asp, Asn, and Arg) modified at three different positions on the surface, which are located in the alpha-helix (Val-110), the beta-sheet (Val-2), and the loop (Val-74), were constructed. Their thermodynamic parameters of denaturation and crystal structures were examined by calorimetry and by x-ray crystallography at 100 K, respectively. The introduced polar residues made hydrogen bonds with protein atoms and/or water molecules, sometimes changing the hydration structure around the mutation site. Changes in the stability of the mutant proteins can be evaluated by a unique equation that considers the conformational changes resulting from the substitutions. Using this analysis, the relationship between the changes in the stabilities and the hydration structures for mutant human lysozymes substituted on the surface could be quantitatively estimated. The analysis indicated that the hydration structure on protein surface plays an important role in determining the conformational stability of the protein.     

Method of modeling protein structure by the two-dimensional nuclear magnetic resonance spectroscopy data; application to the proteinase inhibitor BUSI IIA from bull seminal plasma

A new approach is suggested to model the spatial structure of protein molecules in solution based on combined use of the methods of theoretical conformational analysis and NMR spectroscopy data. At the first stage, special means are used to convert d connectivity information into the most probable values of dihedral angles. This allows search for possible spatial structures in the limited regions of the conformational space at further stages using the methods of the theoretical conformational analysis. The suggested approach was verified in reconstructing the spatial backbone structure of the fragment 17-57 of the proteinase inhibitor BUSI IIA from the bull seminal plasma. The structural model parameters are compared with the corresponding characteristics obtained from the X-ray analysis data for the homologic proteinase inhibitor from the Japanese quail ovomucoid. The suggested approach is shown to correctly reproduce both the general molecule topology and the conformations of individual amino acid residues.     

Determination and comparative analysis of the conformation of bovine pancreatic trypsin inhibitor and trypsin inhibitors E and K from the data of two-dimensional 1H-NMR spectroscopy

On the basis of joint consideration of distance dependences between amide proton NH and protons C alpha H, NH, C beta H of the preceding in amino acid sequence residue from the torsion angles phi psi, chi 1, the correlation diagram of these proton-proton distances with the regions of sterically allowed conformational space (phi, psi) is presented and the method for the determination of the L-amino acid residues backbone conformations is proposed. The diagram was used for the determination of backbone conformations of bovine pancreatic trypsin inhibitor and trypsin inhibitors E and K from Dendroaspis polylepis using the data from two-dimensional 1H-NMR spectroscopy. The analysis of backbone conformations was carried out. The individual elements of these protein molecules secondary structure were characterized and their high conformational homology was shown. The inference about qualitative coincidence of three protein molecules conformation in solution, preservation of secondary structure basic elements and their similarity with bovine pancreatic trypsin inhibitor crystalline structure was made.     

Conformational analysis of dipeptides in aqueous solution. II. Molecular structure of glycine and alanine dipeptides by depolarized rayleigh scattering and laser Raman spectroscopy

A new approach to the experimental conformational analysis of peptides in aqueous solution is presented and discussed. The basic idea is to combine laser Raman spectroscopy and depolarized Rayleigh scattering in order to interpret scattering properties of the dissolved molecule in terms of both local and global structure. We outline a simple method (anisotropic perturbation treatment) appropriate for solving conformational problems in large molecules by studying together slightly perturbed homologous compounds. This method is applied to the study of the molecular structure of simple glycine and alanine dipeptides. The preferred conformation for such molecules is the seven-membered chelated ring (C₇) additionally stabilized by two intermolecular hydrogen bonds involving one molecule of water.     

Exploring the Conformational Behavior of Rigid Porphyrin-Quinone Systems by High-Temperature MD Simulations and Temperature-Dependent 1H-NMR Experiments

Photoinduced electron transfer reactions play an important role in the primary step of the biological photosynthesis process. In an attempt to understand better the mechanism of the charge separation organic donor-acceptor molecules containing porphyrins and quinones were designed as photosynthesis models. In order to study the structure dependence of the photoinduced electron transfer twofold and fourfold bridged porphyrin-quinone systems with increasing donor-acceptor distance were synthesized (Figure 1) [1, 2, 3]. It was assumed that in these molecules the porphyrin and quinone should be linked in a rigid and well-defined orientation. To verify this assumption the conformational behavior of these systems was studied by high-temperature MD simulations in combination with conformational analysis of selected minimized structures [4, 5].     

Structural and rheological characterization of Scleroglucan/borax hydrogel for drug delivery

The polysaccharide Scleroglucan, one of the most rigid polymers found in nature, can form a chemical/physical gel, in the presence of borax. The obtained hydrogel was loaded with three different model molecules (Theophylline, Vitamin B12 and Myoglobin) and then, after freeze-drying, was used as a matrix for tablets. The release profiles of the substances from the dosage forms were evaluated; the matrix appeared capable to modulate the diffusion of the chosen molecules, and different diffusion rates were observed, according to the different radii of the tested molecules. Interestingly, in the dissolution medium the matrix undergoes an anisotropic swelling taking place only in the axial direction, while a negligible radial variation occurs. The water uptake of the matrix occurs according to a Fickian process.

Samples at two different polymer concentrations (0.7 and 2.3%, w/v) were characterized in terms of rheological and mechanical parameters and the properties were interpreted in terms of the molecular structure obtained by conformational analysis.

The flow curves acquired in the viscoelasticity interval, show the effect of the borate ion in improving the resistance of the gel in comparison to the polymer alone. The evaluation of the moduli indicates that the system is viscoelastic, with an appreciable liquid component that increases as the polymer concentration decreases. Also the cohesion of the gel is higher in comparison to the Scleroglucan and is strongly dependent on temperature.

The combination of experimental and theoretical conformational analysis approaches, allowed us to propose a model for the structure of the macromolecular network and to give an explanation to the anomalous swelling that was observed. It came out that the polymer can built up a channel structure, mediated via borax ion interaction, that can accommodate guest molecules of different size.     

Conformational analysis of molecular chains using nano-kinematics

We present algorithms for 3–D manipulation and conforma–tionalanalysis of molecular chains, when bond lengths, bond anglesand related dihedral angles remain fixed. These algorithms areuseful for local deformations of linear molecules, exact ringclosure in cyclic molecules and molecular embedding for shortchains. Other possible applications include structure prediction,protein folding, conformation energy analysis and 3D molecularmatching and docking. The algorithms are applicable to all serialmolecular chains and make no asssumptions about their geometry.We make use of results on direct and inverse kinematics fromrobotics and mechanics literature and show the correspondencebetween kinematics and conformational analysis of molecules.In particular, we pose these problems algebraically and computeall the solutions making use of the structure of these equationsand matrix computations. The algorithms have been implementedand perform well in practice. In particular, they take tensof milliseconds on current workstations for local deformationsand chain closures on molecular chains consisting of six orfewer rotatable dihedral angles     

Conformational analysis of enkephalin analogs containing a disulfide bond. Models for delta- and mu-receptor opioid agonists

Conformational analysis of the cyclic opioids H-Tyr-D-Pen-Gly-Phe-D-Pen-OH (DPDPE) and H-Tyr-D-Cys-Gly-Phe-D-Cys-OH (DCDCE) have been performed using the AMBER program. DPDPE is considerably more selective for delta-receptors than DCDCE. Using the RNGCFM program, a large number of ways were found to close the 14-membered disulfide-containing ring structure. However, intramolecular hydrogen bonds were only possible in gamma-turn and inverse gamma-turn conformations centered on the glycine residue which were associated with opposite chiralities of the disulfide bond. With the cyclic part of the molecules in either a gamma-turn or inverse gamma-turn, a systematic conformational analysis was performed on the tyrosine and phenylalanine sidechains. This showed that conformers with the tyrosine and phenylalanine phenyl rings in the vicinity of the disulfide bond were preferred due to attractive van der Waals forces. For DPDPE, however, this was only possible with a positive dihedral angle for the disulfide bond due to the presence of the beta-carbon methyls of Pen2. In contrast, these preferred conformers were possible with both chiralities of the disulfide bond in DCDCE. Conformational entropies and free energies were computed from the translational, rotational, and vibrational energy levels available to each conformer. The conformational entropies were found to vary significantly and to result in a re-ordering of the lowest energy minima. Based on these conformational differences in DPDPE and DCDCE and their differing pharmacological selectivities, tentative conformational preferences for delta- and mu-receptor opioid peptides are proposed.     

Evidence of Conformational Selection Driving the Formation of Ligand Binding Sites in Protein-Protein Interfaces

Many protein-protein interactions (PPIs) are compelling targets for drug discovery, and in a number of cases can be disrupted by small molecules. The main goal of this study is to examine the mechanism of binding site formation in the interface region of proteins that are PPI targets by comparing ligand-free and ligand-bound structures. To avoid any potential bias, we focus on ensembles of ligand-free protein conformations obtained by nuclear magnetic resonance (NMR) techniques and deposited in the Protein Data Bank, rather than on ensembles specifically generated for this study. The measures used for structure comparison are based on detecting binding hot spots, i.e., protein regions that are major contributors to the binding free energy. The main tool of the analysis is computational solvent mapping, which explores the surface of proteins by docking a large number of small “probe” molecules. Although we consider conformational ensembles obtained by NMR techniques, the analysis is independent of the method used for generating the structures. Finding the energetically most important regions, mapping can identify binding site residues using ligand-free models based on NMR data. In addition, the method selects conformations that are similar to some peptide-bound or ligand-bound structure in terms of the properties of the binding site. This agrees with the conformational selection model of molecular recognition, which assumes such pre-existing conformations. The analysis also shows the maximum level of similarity between unbound and bound states that is achieved without any influence from a ligand. Further shift toward the bound structure assumes protein-peptide or protein-ligand interactions, either selecting higher energy conformations that are not part of the NMR ensemble, or leading to induced fit. Thus, forming the sites in protein-protein interfaces that bind peptides and can be targeted by small ligands always includes conformational selection, although other recognition mechanisms may also be involved.     

Lincomycin and clindamycin conformations. A fragment shared by macrolides, ketolides and lincosamides determined from TRNOE ribosome-bound conformations

Two important lincosamide antibiotics, lincomycin and clindamycin were studied in the complex state with the bacterial ribosome after a conformational analysis by 1H and 13C NMR spectroscopy and molecular modelling of the unbound molecules. Lincosamide-ribosome interactions were investigated using two-dimensional transferred nuclear Overhauser effect spectroscopy (TRNOESY), resulting in a bound structure compatible with the experimental NMR data. The results compared with the conformational analysis of the substrates in solution indicate that specific conformations are preferred in the bound state. Clindamycin, the more bioactive antibiotic studied, displayed a stronger NMR response than lincomycin showing that in lincosamide-ribosome interactions, a low affinity binding level is associated to the tight binding one and is related to biological activity. This study shows that conformation plays an essential role for the low affinity binding site. Superimposition of lincosamide, macrolide and ketolide bound structures exhibited conformational similarities in a particular fragment which is in agreement with a hypothesis of partial overlapping lincosamide and macrolide binding sites.     

Spatial structure of isoleucine pentapeptides Glu-Phe-Leu-Arg-Ile-NH2 and Pro-Phe-Tyr-Arg-Ile-NH2

The spatial structure of two cardioactive isoleucine pentapeptides Glu-Phe-Leu-Arg-Ile-NH2 (I) and Pro-Phe-Tyr-Arg-Ile-NH2 (II) have been investigated using the theoretical conformational analysis. The low-energy conformations of these molecules were found, the values of dihedral angles of the backbone and side chains of the amino acid residues constituting these peptides were determined, and the energies of intra- and interresidual interactions were estimated. It was revealed that the spatial structure of molecule I can exist as five and that of molecule II as seven stable backbone forms.     

Effect of high hydrostatic pressure on hydration and activity of ribozymes

Formation and stabilization of RNA structure in the cell depends on its interaction with solvent and metal ions. High hydrostatic pressure (HHP) is a convenient tool in an analysis of the role of small molecules in the structure stabilization of biological macromolecules. Analysis of HHP effect and various concentrations of ions showed that water induce formation of the active ribozyme structure. So, it is clear that water is the driving force of conformational changes of nucleic acid.     

Electron microscopy studies of alpha 2-macroglobulin conformational intermediates obtained by derivatization with cis-dichlorodiammineplatinum (II)

The structure of human alpha 2-macroglobulin (alpha 2M) after reaction with cis-dichlorodiammineplatinum (II) (cis-DDP) was studied by electron microscopy. The cis-DDP stabilized a novel conformation of the native inhibitor resembling a doughnut surrounded by two, three, of four well defined spherules. When only two spherules were present, these structures were usually oriented on opposite sides of the doughnut. The protein region joining a spherule to the central structure did not include sufficient mass to exclude stain and was, therefore, invisible. Other images showed spherules that were partially superimposed on the doughnut. A comparison of many molecules suggested great flexibility of the peripheral spherules relative to the central structure. The cis-DDP prevented complete conformational change when the alpha 2M was reacted with trypsin. The products of this reaction included apparent conformational intermediates. These intermediates most closely resembled either native alpha 2M or the well established "H" structure of alpha 2M-proteinase, depending on the initial conditions used to modify the alpha 2 M with cis-DDP. When cis-DDP-treated alpha 2M was reacted with trypsin, purified by chromatography and subsequently treated with diethyldithiocarbamate, complete conformational change was observed. Based on an analysis of the alpha 2M structural intermediates obtained using the chemical modification procedures described here, a new model of alpha 2M conformational change was developed. We postulate that conformational change initially involves contraction of the peripheral spherules towards the central doughnut. These spherules then unfold and elongate in the perpendicular direction to form the lateral walls of the proteinase transformed alpha 2M H structure.     

Mechanism of action of aspartic proteases. IV.Conformational characteristics of a substrate and an inhibitor of rhizopuspepsin ]

On the basis of theoretical conformational analysis of separate peptide fragments, the conformational characteristics of two substrates and a substrate-like inhibitor of aspartic protease rhizopuspepsin were studied. It was shown that the spatial structure of these molecules is described by several families of conformations, the transition between which does not require the overcoming of high energy barriers. It was assumed that the stabilization of beta-structural conformations experimentally observed in inhibitor complexes is due to the greater predisposition of extended structures to the formation of effective intermolecular contacts with amino acid residues of the active site of the enzyme.     

Interactions of 4,4′-diaminoazobenzene derivatives with telomeric G-quadruplex DNA

The development of small molecules to stabilize the G-quadruplex structure has garnered significant attention for anticancer drug discovery. Herein, we report the synthesis of several 4,4′-diaminoazobenzene derivatives containing different substituent groups and their ability to bind and stabilize telomeric G-quadruplex DNA. Circular dichroism (CD) spectroscopy was performed to characterize the quadruplex topologies, measure stabilization effects, and evaluate their capabilities for conformational photoregulation. 4,4′-Diaminoazobenzene derivatives were found to moderately stabilize quadruplex structures but not affect conformational photoregulation. This work further develops the design and general understanding of the stabilization effects of small molecules with telomeric G-quadruplex DNA.     

Molecular dynamics study of water penetration in staphylococcal nuclease

The ionization properties of Lys and Glu residues buried in the hydrophobic core of staphylococcal nuclease (SN) suggest that the interior of this protein behaves as a highly polarizable medium with an apparent dielectric constant near 10. This has been rationalized previously in terms of localized conformational relaxation concomitant with the ionization of the internal residue, and with contributions by internal water molecules. Paradoxically, the crystal structure of the SN V66E variant shows internal water molecules and the structure of the V66K variant does not. To assess the structural and dynamical character of interior water molecules in SN, a series of 10-ns-long molecular dynamics (MD) simulations was performed with wild-type SN, and with the V66E and V66K variants with Glu66 and Lys66 in the neutral form. Internal water molecules were identified based on their coordination state and characterized in terms of their residence times, average location, dipole moment fluctuations, hydrogen bonding interactions, and interaction energies. The locations of the water molecules that have residence times of several nanoseconds and display small mean-square displacements agree well with the locations of crystallographically observed water molecules. Additional, relatively disordered water molecules that are not observed crystallographically were found in internal hydrophobic locations. All of the interior water molecules that were analyzed in detail displayed a distribution of interaction energies with higher mean value and narrower width than a bulk water molecule. This underscores the importance of protein dynamics for hydration of the protein interior. Further analysis of the MD trajectories revealed that the fluctuations in the protein structure (especially the loop elements) can strongly influence protein hydration by changing the patterns or strengths of hydrogen bonding interactions between water molecules and the protein. To investigate the dynamical response of the protein to burial of charged groups in the protein interior, MD simulations were performed with Glu66 and Lys66 in the charged state. Overall, the MD simulations suggest that a conformational change rather than internal water molecules is the dominant determinant of the high apparent polarizability of the protein interior.     

The crystal and molecular structure of the anticancer drug actinomycin D--some explanations for its unusual properties

The crystal structure of the antitumor antibiotic actinomycin D has been determined by the methods of x-ray crystallography. There are three independent molecules in the asymmetric unit. Two of the molecules form a hydrogen-bonded dimer. The peptides within all three molecules have very similar conformations. The greatest conformational variability in the drug molecules occurs in the torsion angles of the bonds connecting the phenoxazone ring to the peptide rings. The results of this analysis has allowed us to explain the unusual physical properties of ActD as well as to provide an explanation for the thermodynamics of its interactions with DNA.     

Computer simulated modeling of biomolecular systems.

This paper describes the algorithm of a program used to simulate three dimensional models of molecules. In addition to open ended molecules the program also enables simulation of structures with constraints in the form of cyclic regions or fixed location of particular atoms. Several molecules can be handled in a single run and each molecule can have any number of contraints. Further, any number of conformations can be obtained for each constrained region. The program can be used for research in several areas of molecular biology, e.g., structure determination, conformational analysis and topographic comparisons.