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N Go

Publications and source records attributed to N Go.

At least 37 records · Page 2Linked to original sources
PubMed1994

Biological meaning, statistical significance, and classification of local spatial similarities in nonhomologous proteins.

We have completed an exhaustive search for the common spatial arrangements of backbone fragments (SARFs) in nonhomologous proteins. This type of local structural similarity, incorporating short fragments of backbone atoms, arranged not necessarily in the same order along the polypeptide chain, appears to be important for protein function and stability. To estimate the statistical significance of the similarities, we have introduced a similarity score. We present several locally similar structures, with a large similarity score, which have not yet been reported. On the basis of the results of pairwise comparison, we have performed hierarchical cluster analysis of protein structures. Our analysis is not limited by comparison of single chains but also includes complex molecules consisting of several subunits. The SARFs with backbone fragments from different polypeptide chains provide a stable interaction between subunits in protein molecules. In many cases the active site of enzyme is located at the same position relative to the common SARFs, implying a function of the certain SARFs as a universal interface of the protein-substrate interaction.

Binding Sites↗
PubMed1994

Harmonic and anharmonic aspects in the dynamics of BPTI: a normal mode analysis and principal component analysis.

A comparison is made between a 200-ps molecular dynamics simulation in vacuum and a normal mode analysis on the protein bovine pancreatic trypsin inhibitor (BPTI) in order to elucidate the dual aspects of harmonicity and anharmonicity in the dynamics of proteins. The molecular dynamics trajectory is analyzed using principal component analysis, an effective harmonic analysis suited for comparison with the results from the normal mode analysis. The results suggest that the first principal component shows qualitatively different behavior from higher principal components and is associated with apparent barrier crossing events on an anharmonic conformational energy surface. The higher principal components appear to have probability distributions that are well approximated by Gaussians, indicating harmonicity. Eliminating the contribution from the first principal component reveals a great deal of correspondence between the 2 methods. This correspondence, however, involves a factor of 2, as the variances of the distribution of the higher principal components are, on average, roughly twice those found from the normal mode analysis. A model is proposed to reconcile these results with those from previous analyses.

Aprotinin↗
PubMed1994

Collective motions in proteins investigated by X-ray diffuse scattering.

We have developed theoretical models for analysis of X-ray diffuse scattering from protein crystals. A series of models are proposed to be used for experimental data with different degrees of precision. First, we propose the normal mode model, where conformational dynamics of a protein is assumed to occur mostly in a limited conformational subspace spanned by a small number of low-frequency normal modes in the protein. When high precision data are available, variances and covariances of the normal mode variables can be determined from experimental data using this model. For experimental data with lower degrees of precision, we introduce a series of simpler models. These models express the covariance matrix using relatively simple empirical correlation functions by assuming the correlation between a pair of atoms to be isotropic. As an application of these simpler models, we calculate diffuse-scattering patterns from a human lysozyme crystal to examine how each adjustable parameter in the models affects general features of the resulting patterns. The results of the calculation are summarized as follows. (1) The higher order scattering makes a significant contribution at high resolutions. (2) The resulting simulated patterns are sensitive to changes in correlation lengths of about 1 A, as well as to changes of the functional form of the correlation function. (3) But only the "average" value of the intra- and intermolecular correlation lengths seems to determine the gross features of the pattern. (4) The effect of the atom-dependent amplitude of fluctuations is difficult to observe.

Computer Simulation↗
PubMed1994

Dynamic structure of human lysozyme derived from X-ray crystallography: normal mode refinement.

X-ray crystallography provides a wealth of information about the dynamic as well as static protein structure. A new method of dynamic structure refinement of protein X-ray crystallography, normal mode refinement, is proposed. In this method, the Debye-Waller factor is expanded in terms of the low-frequency internal normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. The internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their inter-atomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analyses of experimental data of human lysozyme and its mutant, C77A/C95A, to reveal its dynamic structure.

Crystallography, X-Ray↗
PubMed1993

Effect of solvent on collective motions in globular protein.

Two molecular dynamics simulations on bovine pancreatic trypsin inhibitor (BPTI), have been made, one in vacuum, the other in water, in order to assess the effect of the solvent water on collective motions. Principal component analysis has been performed to determine collective modes, the principal components, which are assumed to behave as effectively independent harmonic oscillators. Projection of the protein's motion in water onto the plane defined by the first two principal components shows a clustering effect in the trajectory, absent in the vacuum trajectory. This is thought to be due to many local minima in the free energy surface caused by solute-solvent interactions. In order to assess the viscous effect of the solvent, friction coefficients for the principal components were determined by analyzing their velocity correlation functions in terms of the Langevin equation for an independent damped oscillator. Consistent with this analysis is that all modes have friction coefficients centered on the value of 47 cm-1 in a range of +/- 10 cm-1. With this friction coefficient, all modes of effective frequencies below 23.5 cm-1 display overdamped motion. By assuming the harmonic approximation for the conformational energy surface for BPTI in vacuum to be valid for BPTI in water, and treating each mode as an independent damped oscillator with a friction coefficient of 47 cm-1, the shift to higher frequencies in the water spectrum relative to the vacuum spectrum could be almost exactly reproduced, indicating this shift is due solely to the viscous effect of the solvent. By analyzing the time correlation functions of the first four principal components it is found that they can be very well described as independent damped oscillators each with a friction coefficient of 47 cm-1.

Animals↗
PubMed1993

Conformational deformation in deoxymyoglobin by hydrostatic pressure.

Pressure effect on the equilibrium conformation in sperm whale deoxymyoglobin and its volume fluctuation are studied by the normal mode analysis and strain tensor analysis. The pressure-induced deformation of interhelix regions are found to be remarkably more compressed than the other parts of the molecule. The intrahelix compressibility is shown to be relatively small. We also calculate the compressibility of the three hydrophobic clusters, located at the bottom, distal, and proximal side of the heme. Its value is found to decrease in the indicated order. The average compressibility of these hydrophobic clusters is less than the average interhelix compressibility, even though there are large cavities in these clusters. In order to study overall deformation, we define a linear compressibility and calculate it for all pairs of C alpha atoms. The pressure-induced deformation is observed to be heterogeneous also in this analysis. The calculated root-mean-square displacement of the constituent atoms in the equilibrium conformation at 1,000 atm from those at 0 atm is 0.12 A, which is much smaller in magnitude than the average value of the atomic fluctuations at room temperature. In the water solvent, the volume excluded by the protein molecule in the equilibrium conformation is reduced by 0.9%, when the pressure is raised from 0 to 1,000 atm. The calculated magnitude of the root-mean-square volume fluctuation is 0.3% of the excluded volume at room temperature. The square of the volume fluctuation is given as a sum of contributions from individual normal modes. Contributions from low frequency normal modes are found to dominate over those from higher frequency normal modes. The estimated value of the isothermal compressibility of deoxymyoglobin is 9.37 x 10(-12) cm2/dyn.

Animals↗
PubMed1993

Secondary structural features of modules M2 and M3 of barnase in solution by NMR experiment and distance geometry calculation.

Proteins consist of structural units such as globular domains, secondary structures, and modules. Modules were originally defined by partitioning a globular domain into compact regions, each of which is a contiguous polypeptide segment having a compact conformation. Since modules show close correlations with the intron positions of genes, they are regarded as primordial polypeptide pieces encoded by exons and shuffled, leading to yield new combination of them in early biological evolution. Do modules maintain their native conformations in solution when they are excised at their boundaries? In order to find answers to this question, we have synthesized modules of barnase, one of the bacterial RNases, and studied the solution structures of modules M2 (amino acid residues 24-52) and M3 (52-73) by 2D NMR studies. Some local secondary structures, alpha-helix, and beta-turns in M2 and beta-turns in M3, were observed in the modules at the similar positions to those in the intact barnase but the overall state seems to be in a mixture of random and native conformations. The present result shows that the excised modules have propensity to form similar secondary structures to those of the intact barnase.

Amino Acid Sequence↗
PubMed1993

Normal mode analysis of mouse epidermal growth factor: characterization of the harmonic motion.

Normal mode analysis of mouse epidermal growth factor (mEGF) has been carried out at room temperature. The value of the lowest frequency is 4.1 cm-1. This mode corresponds to hinge-bending motion between the N-terminal and C-terminal domains of mEGF. This hinge-bending motion corresponds to the "mitten mode." In this motion, the N-terminal domain is almost rigid. However, the C-terminal domain is found to consist of three rigid segments. Two segments, C33-D46 and G51-R53, are observed moving in the same direction, but L47-W50 moves in the opposite direction. For this mode, the effective Young's modulus turned out to be 1.1 x 10(9) dyn.cm-2. This value is a little larger than that of the mode with the lowest frequency 4.4 cm-1 of BPTI. The difference may be related to the fraction of residues involved in beta-sheets in the molecule. Similar analyses are carried out for other low frequency modes.

Animals↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure. I. Theory and test by simulated diffraction data.

A dynamic structure refinement method for X-ray crystallography, referred to as the normal mode refinement, is proposed. The Debye-Waller factor is expanded in terms of the low-frequency normal modes whose amplitudes and eigenvectors are experimentally optimized in the process of the crystallographic refinement. In this model, the atomic fluctuations are treated as anisotropic and concerted. The normal modes of the external motion (TLS model) are also introduced to cover the factors other than the internal fluctuations, such as the lattice disorder and diffusion. A program for the normal mode refinement (NM-REF) has been developed. The method has first been tested against simulated diffraction data for human lysozyme calculated by a Monte Carlo simulation. Applications of the method have demonstrated that the normal mode refinement has: (1) improved the fitting to the diffraction data, even with fewer adjustable parameters; (2) distinguished internal fluctuations from external ones; (3) determined anisotropic thermal factors; and (4) identified concerted fluctuations in the protein molecule.

Humans↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure. II. Application to human lysozyme.

The dynamic structure of a protein, human lysozyme, is determined by the normal mode refinement of X-ray crystal structure. This method uses the normal modes of both internal and external motions to distinguish the real internal dynamics from the external terms such as lattice disorder, and gives an anisotropic and concerted picture of atomic fluctuations. The refinement is carried out with diffraction data of 5.0 to 1.8 A resolution, which are collected on an imaging plate. The results of the refinement show: (1) Debye-Waller factor consists of two parts, highly anisotropic internal fluctuations and almost isotropic external terms. The former is smaller than the latter by a factor of 0.72 in the scale of B-factor. Therefore, the internal dynamics cannot be recognized directly from the apparent electron density distribution. (2) The internal fluctuations show basically similar features as those predicted by the normal mode analysis, with almost the same amplitude and a similar level of anisotropy. (3) Correlations of fluctuations are detected between two lobes forming the active site cleft, which move simultaneously in opposite directions. This corresponds to the hinge-bending motion of lysozyme.

Humans↗
PubMed1992

Common spatial arrangements of backbone fragments in homologous and non-homologous proteins.

We have developed a new method of detecting common spatial arrangements of backbone fragments in proteins. This method allows corresponding fragments to occur in a different order in respective amino acid sequences. We applied this method to detect structural similarities between an acid protease, endothiapepsin, and all other proteins in the protein data bank. Significant similarities were found not only with other acid proteases but also with virus proteases and with proteins having different functions. The possible biological meaning of these similarities is discussed.

Aspartic Acid Endopeptidases↗
PubMed1992

Normal mode refinement: crystallographic refinement of protein dynamic structure applied to human lysozyme.

A new method of dynamic structure refinement of protein x-ray crystallography, normal mode refinement, is developed. In this method the Debye-Waller factor is expanded in terms of the low-frequency normal modes and external normal modes, whose amplitudes and couplings are optimized in the process of crystallographic refinement. By this method, internal and external contributions to the atomic fluctuations can be separated. Also, anisotropic atomic fluctuations and their interatomic correlations can be determined experimentally even with a relatively small number of adjustable parameters. The method is applied to the analysis of experimental data of human lysozyme to reveal its dynamic structure.

Humans↗
PubMed1992

Ly-1 B (B-1) cells are the main source of B cell-derived interleukin 10.

We have previously reported (O'Garra, A. et al., Int. Immunol. 1990, 2:821) that murine B lymphomas and purified normal peritoneal B cells produce interleukin (IL) 10. We now show that this production of IL 10 B cells correlates with the presence of Ly-1 (B-1) B cells, in both normal and diseased mice. Using a semi-quantitative modification of the polymerase chain reaction, we show that IL 10 expression is detectable in peritoneal B cells but only becomes apparent in splenic B cells of aged mice of which a high proportion are Ly-1+. Furthermore, the expression of IL 10 is constitutive in splenic B cells from mice carrying the Ly-1+ BCL1 lymphoma. Since IL 10 is a potent regulator of in vitro immune function, its production by Ly-1 lineage B (B-1) cells raises the possibility that this subset of B cells may regulate their own development and/or the function of other immunocompetent cells.

Aging↗
PubMed1992

Survey of conformational role of ester bonds in a cyclic depsipeptide. Study on cyclo(-L-Ala-L-Hmb-)2 by energy calculation and NMR spectroscopy.

The effect of ester bond on the conformation of peptide molecule was studied by designing and synthesizing a model tetradepsipeptide cyclo(-L-Ala-L-Hmb-)2 and by analyzing the conformation both theoretically and experimentally. Theoretical analysis showed that both ester and peptide bonds in the calculated low-energy conformations within 3 kcal/mol of the global minimum take a trans but distorted configuration. The distortion is larger in ester bonds than in peptide bonds. Further, the four carbonyls project from one side of the plane of the cyclic backbone, whereas the side chains project from the other side. These results are consistent with the experimental results obtained by NMR measurement; first, the coupling constant deduced from 1H-NMR species in DMSO-d6 is consistent with the dihedral angles of the calculated low-energy conformations; second, results of NOE measurement can reproduce the calculated configuration of the carbonyls and side chains. From the consistency between theoretical and experimental results, it is concluded that this model tetradepsipeptide takes an all-trans backbone conformation in solution and this backbone conformation is stabilized by large distortion in the ester bond, which compensates the strain resulted from the 12-membered cyclic backbone structure consisting only of L-residues.

Amino Acid Sequence↗
PubMed1991

Refined structure of melittin bound to perdeuterated dodecylphosphocholine micelles as studied by 2D-NMR and distance geometry calculation.

In our previous paper we reported the conformation of melittin bound to perdeuterated dodecylphosphocholine micelles as studied by 1H NMR experiment and distance geometry calculation. No hydrogen bonds were taken into consideration explicitly in the calculation. However, mostly alpha-helical conformations were obtained as results of the calculation even with no explicitly assumed hydrogen bonds. In the present paper we refined the distance geometry calculation by incorporating hydrogen bonds suggested by the previous calculation. As a result, we obtained the conformation of melittin, which was consistent with both NMR data and the additional hydrogen bonding data. The alpha-helical rod in the refined conformation also has a kink at Thr-11 and Gly-12, but its bent angle is now a bit narrowly distributed in 135 degrees +/- 15 degrees. In the present study another distortion at Trp-19 and IIe-20 becomes conspicuous. The average root-mean-square displacement of atoms is now much smaller and is 1.5 A for all backbone atoms. In the present paper side chain conformations are also analyzed.

Deuterium↗
PubMed1991

Projection of Monte Carlo and molecular dynamics trajectories onto the normal mode axes: human lysozyme.

A method is presented to describe the internal motions of proteins obtained from molecular dynamics or Monte Carlo simulations as motions of normal mode variables. This method calculates normal mode variables by projecting trajectories of these simulations onto the axes of normal modes and expresses the trajectories as a linear combination of normal mode variables. This method is applied to the result of the molecular dynamics and the Monte Carlo simulations of human lysozyme. The motion of the lowest frequency mode extracted from the simulations represents the hinge bending motion very faithfully. Analysis of the obtained motions of the normal mode variables provides an explanation of the anharmonic aspects of protein dynamics as due first to the anharmonicity of the actual potential energy surface near a minimum and second to trans-minimum conformational changes.

Binding Sites↗
PubMed1990

Deoxymyoglobin studied by the conformational normal mode analysis. I. Dynamics of globin and the heme-globin interaction.

Dynamic properties of deoxymyoglobin are studied theoretically by the analysis of conformational fluctuations. Root-mean-square atomic fluctuations and distance fluctuations between different segments reveal the mechanical construction of the molecule. Eight alpha-helices behave as relatively rigid bodies and corner regions are more flexible, showing larger fluctuations. More particularly, corner regions EF and GH are specific in that flanking alpha-helices extend their rigidity up to a point in the corner region and the two rigid segments are connected flexibly at that point. The FG corner is exceptional. A segment from the F helix to the beginning of the G helix, in which the FG corner is included, becomes relatively rigid by means of strong interactions with the heme group. The whole myoglobin molecule is divided into two large units of motion, one extending from the B to the E helix, and the other from the F to the H helix. These two units are connected covalently by the EF corner. However, dynamic interactions between these two units take place mainly through contacts between helices B and G and not through the EF corner. From correlation coefficients between fluctuational motions of residues and the heme group, 55 residues are identified as having strong dynamic interactions with the heme moiety. Among them, 18 residues in the three segments, one consisting of residues from the C helix to the CD corner, a second consisting of the E helix, and a third from the F helix to the beginning of the G helix, are in close contact with the heme group. Twenty-two of the 55 residues are within four residues of the 18 residues in their sequential residue number and are more than 3 A away from the heme group. The other 15 residues are located further in the sequential residue number and are all found in helices A and H. They are more than 6 A away from the heme group. By the use of correlation coefficients of fluctuations between residues, it is found that dynamic interaction with the heme group is transmitted to the A helix and the beginning of the H helix in the direction Leu(E15)----[Val(All) and Trp(A12)]. The transmission to the C-terminal end of the H helix is mediated by a long segment, from the end of the EF corner to the beginning of the G helix, that lies on the heme group and has close contacts over a wide range.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗