New measures for estimating surface complementarity and packing at protein-protein interfaces

A number of methods exist that use different approaches to assess geometric properties like the surface complementarity and atom packing at the protein-protein interface. We have developed two new and conceptually different measures using the Delaunay tessellation and interface slice selection to compute the surface complementarity and atom packing at the protein-protein interface in a straightforward manner. Our measures show a strong correlation among themselves and with other existing measures, and can be calculated in a highly time-efficient manner. The measures are discriminative for evaluating biological, as well as non-biological protein-protein contacts, especially from large protein complexes and large-scale structural studies (http://pallab.serc.iisc.ernet.in/nip_nsc).     

Hydrophobic patches on protein subunit interfaces: Characteristics and prediction

Hydrophobic patches, defined as clusters of neighboring apolar atoms deemed accessible on a given protein surface, have been investigated on protein subunit interfaces. The data were taken from known tertiary structures of multimeric protein complexes. Amino acid composition and preference, patch size distribution, and patch contact complementarity across associating subunits were examined and compared with hydrophobic patches found on the solvent-accessible surface of the multimeric complexes. The largest or second largest patch on the accessible surface of the entire subunit was involved in multimeric interfaces in 90% of the cases. These results should prove useful for subunit design and engineering as well as for prediction of subunit interface regions. Proteins 28:333–343, 1997. © 1997 Wiley-Liss, Inc.     

A dissection of specific and non-specific protein-protein interfaces

We compare the geometric and physical-chemical properties of interfaces involved in specific and non-specific protein-protein interactions in crystal structures reported in the Protein Data Bank. Specific interactions are illustrated by 70 protein-protein complexes and by subunit contacts in 122 homodimeric proteins; non-specific interactions are illustrated by 188 pairs of monomeric proteins making crystal-packing contacts selected to bury more than 800 A2 of protein surface. A majority of these pairs have 2-fold symmetry and form crystal dimers that cannot be distinguished from real dimers on the basis of the interface size or symmetry. The chemical and amino acid compositions of the large crystal-packing interfaces resemble the protein solvent-accessible surface. These interfaces are less hydrophobic than in homodimers and contain much fewer fully buried atoms. We develop a residue propensity score and a hydrophobic interaction score to assess preferences seen in the chemical and amino acid compositions of the different types of interfaces, and we derive indexes to evaluate the atomic packing, which we find to be less compact at non-specific than at specific interfaces. We test the capacity of these parameters to identify homodimeric proteins in crystal structures, and show that a simple combination of the non-polar interface area and the fraction of buried interface atoms assigns the quaternary structure of 88% of the homodimers and 77% of the monomers in our data set correctly. These success rates increase to 93-95% when the residue propensity score of the interfaces is taken into consideration.     

Biological units and their effect upon the properties and prediction of protein-protein interactions

Structural data as collated in the Protein Data Bank (PDB) have been widely applied in the study and prediction of protein-protein interactions. However, since the basic PDB Entries contain only the contents of the asymmetric unit rather than the biological unit, some key interactions may be missed by analysing only the PDB Entry. A total of 69,054 SCOP (Structural Classification of Proteins) domains were examined systematically to identify the number of additional novel interacting domain pairs and interfaces found by considering the biological unit as stored in the PQS (Protein Quaternary Structure) database. The PQS data adds 25,965 interacting domain pairs to those seen in the PDB Entries to give a total of 61,783 redundant interacting domain pairs. Redundancy filtering at the level of the SCOP family shows PQS to increase the number of novel interacting domain-family pairs by 302 (13.3%) from 2277, but only 16/302 (1.4%) of the interacting domain pairs have the two domains in different SCOP families. This suggests the biological units add little to the elucidation of novel biological interaction networks. However, when the orientation of the domain pairs is considered, the PQS data increases the number of novel domain-domain interfaces observed by 1455 (34.5%) to give 5677 non-redundant domain-domain interfaces. In all, 162/1455 novel domain-domain interfaces are between domains from different families, an increase of 8.9% over the PDB Entries. Overall, the PQS biological units provide a rich source of novel domain-domain interfaces that are not seen in the studied PDB Entries, and so PQS domain-domain interaction data should be exploited wherever possible in the analysis and prediction of protein-protein interactions.     

A multivariate study of the relationship between the genetic code and the physical-chemical properties of amino acids

Summary The 20 naturally occurring amino acids are characterized by 20 variables: pK_{NH 2}, pK_COOH, pI, molecular weight, substituent van der Waals volume, seven¹H and¹³C nuclear magnetic resonance shift variables, and eight hydrophobicity-hydrophilicity scales. The 20-dimensional data set is reduced to a few new dimensions by principal components analysis. The three first principal components reveal relationships between the properties of the amino acids and the genetic code. Thus the amino acids coded for by adenosine (A), uracil (U), or cytosine (C) in their second codon position (corresponding to U, A, or G in the second anticodon position) are grouped in these components. No grouping was detected for the amino acids coded for by guanine (G) in the second codon position (corresponding to C in the second anticodon position). The results show that a relationship exists between the physical-chemical properties of the amino acids and which of the A (U), U (A), or C (G) nucleotide is used in the second codon (anticodon) position. The amino acids coded for by G (C) in the second codon (anticodon) position do not participate in this relationship.     

Improvement of the synthesis and pharmacokinetic properties of chromenotriazolopyrimidine MDM2-p53 protein-protein inhibitors

Human murine double minute 2 (MDM2) is a negative regulator of p53, which plays an important role in cell cycle and apoptosis. We report several optimizations to the synthesis of the chromenotriazolopyrimidine series of MDM2-p53 protein-protein interaction inhibitors. Additionally, the in vitro and in vivo stability, pharmacokinetic properties and solubility were improved through N-substitution.     

蛋白质表面氨基酸特性研究进展

分布在蛋白质分子表面的暴露于溶剂的氨基酸所具有的一些特性对蛋白质的折叠和聚合过程、蛋白质一蛋白质相互作用以及蛋白质的功能具有重要影响。本文分析了蛋白质表面氨基酸在疏水性、保守性、静电势及结构方面的一些特性,阐述了近年来国际上利用这些特性对蛋白质一蛋白质相互作用界面进行预测的方法,最后介绍了几款预测蛋白质表面氨基酸的软件。     

Soil properties along altitudinal gradient in Himalayan temperate forest of Garhwal region

The aim of the present study was to analyse the soil properties in different seasons at varying altitudes. The study was carried out in Dhanaulti forest, falls under temperate region of Garhwal Himalaya in Uttarakhand State, India. Physical properties and chemical properties of the soil were estimated using all standard procedures. In the present study, sand particles were reported highest (77.21%) in rainy season followed by in summer (70.17%) and winter (63.15%) seasons. The silt and clay particles also followed similar trend as sand which reduced in order of rainy > summer > winter seasons. The water holding capacity of soil ranged from 62.13 to 67.70%. The majority of soils were dark brown to dark yellowish brown in colour, which is considered having higher potential of water holding capacity. The values of nitrogen ranged between 0.01 to 0.012% (upper altitude), 0.009 to 0.011% (middle altitude) and 0.007 to 0.011% (lower altitude). The effects of altitudes and seasons in nitrogen show significant variation. Potassium ranged between 102.29 and 206.22 kg ha^? 1. The combined effect of season and soil-depth also showed significant variation in level of potassium. The soil organic carbon values were between 0.14 and 0.19% and pH values ranged between 6.33 and 6.75 which was slightly acidic in nature.     

Studies on molecular properties prediction,antitubercular and antimicrobial activities of novel quinoline based pyrimidine motifs

In the present study, a series of 3-((6-(2,6-dichloroquinolin-3-yl)-4-aryl-1,6-dihydro-pyrimidin-2-yl)thio)propanenitriles 5a–o were synthesized and subjected to molecular properties prediction and drug-likeness model score by Molinspiration property calculation toolkit and MolSoft software, respectively. Compound 5m (4-OCH₃) was found to be maximum drug-likeness model score (0.42). Among the screened compounds, 5m showed the most promising antitubercular activity with MIC of 0.20 μg/mL, while compounds 5g, 5k and 5m displayed broad spectrum antibacterial activity against all the bacterial strains. Moreover, compound 5k was found to be the most potent antifungal agent. Further, the results of preliminary MTT cytotoxicity studies on HeLa cells suggested that potent antimicrobial activity of 5g, 5k and 5m was escorted by low cytotoxicity.     

Molecular properties prediction and synthesis of novel 1,3,4-oxadiazole analogues as potent antimicrobial and antitubercular agents

In the present investigation, a series of 1,5-dimethyl-2-phenyl-4-{[(5-aryl-1,3,4-oxadiazol-2-yl)methyl]amino}-1,2-dihydro-3H-pyrazol-3-one were subjected to molecular properties prediction, drug-likeness by Molinspiration (Molinspiration, 2008) and MolSoft (MolSoft, 2007) software, lipophilicity and solubility parameters using ALOGPS 2.1 program. The compounds followed the Lipinski ‘Rule of five’ were synthesized for antimicrobial and antitubercular screening as oral bioavailable drugs/leads. Maximum drug-likeness model score (0.95) was found for compound, 4a. All the synthesized compounds were characterized by IR, NMR and mass spectral analysis followed by antimicrobial and antimycobacterial screening. Among the title compounds, compound 4d showed pronounced activity against Mycobacterium tuberculosis H₃₇Rv and isoniazid resistant M. tuberculosis (INHR-TB) with minimum inhibitory concentrations (MICs) 0.78 μM and 1.52 μM, respectively. The compound, 4a showed maximum activity against all bacterial strains with MIC 4–8 μg/mL comparable to standard drug ciprofloxacin, while the compounds, 4e and 4k showed maximum antifungal activity with MIC 8–16 μg/mL less active than standard drug fluconazole.     

Statistical analysis and prediction of the exonic structure of human genes

Summary Nonhomologous fully sequenced human protein-coding genes were studied. Three sets of exon-exon junctions were formed defined by the intron (shadow) position relative to the reading frame. For the analysis of intron shadow signals in exons, information content and discrimination energy approaches were used with the correction allowing one to ignore the influence of a protein-coding message. The corrected formulas allow one to define the consensuses for the three types of intron shadow signals as aAG/guwn, cAG/GUnn, and cAG/gunU, and provide better recognition than the original formulas. The analysis of the codon usage in the signal positions leads to the conclusion that the prevalence of some amino acids in corresponding protein sites is caused by the signal requirements and not vice versa. The distribution of potential intron shadow signals in exons contradicts the hypothesis of intron insertion into suitable preexisting sites. There exists a correlation between the intron types and/or the exon length modulo 3.     

Statistical properties of the Jukes-Holmquist method of estimating the number of nucleotide substitutions: Reply to Holmquist and Conroy's criticism

Summary Conducting computer simulations, Nei and Tateno (1978) have shown that Jukes and Holmquist's (1972) method of estimating the number of nucleotide substitutions tends to give an overestimate and the estimate obtained has a large variance. Holmquist and Conroy (1980) repeated some parts of our simulation and claim that the overestimation of nucleotide substitutions in our paper occurred mainly because we used selected data. Examination of Holmquist and Conroy's simulation indicates that their results are essentially the same as ours when the Jukes-Holmquist method is used, but since they used a different method of computation their estimates of nucleotide substitutions differed substantially from ours. Another problem in Holmquist and Conroy's Letter is that they confused the expected number of nucleotide substitution with the number in a sample. This confusion has resulted in a number of unnecessary arguments. They also criticized ourX₂ measure, but this criticism is apparently due to a misunderstanding of the assumptions of our method and a failure to use our method in the way we described. We believe that our earlier conclusions remain unchanged.     

Tannin-based rigid foams: A survey of chemical and physical properties

Tannin-based rigid foams, prepared from 95% natural material, are suggested for replacing synthetic phenol–formaldehyde foams in various applications. For that purpose, a few physical properties were measured and reported here: resistance to fire and chemicals, absorption of various liquids, permeability, thermal conductivity and mechanical (compressive and tensile) strength. Modifying the composition through the use of boric and/or phosphoric acid allowed substantial increase of fire resistance. The materials were also found to present good resistance to strong acid and bases, and to solvents. High affinity for water, but limited one for organic liquids, was also evidenced. Finally, slightly anisotropic mechanical properties were measured. The materials present a brittle behaviour, whether tested in compression or traction; nevertheless, their strengths, as well as their thermal conductivities, are fully comparable with those of their phenolic counterparts. We show that such materials of vegetable origins can compete with synthetic ones for most of traditional applications.     

Computational analysis and prediction for exons of PAC579 genomic sequence

To isolate the novel genes related to human hepatocellular carcinoma (HCC), we sequenced P1-derived artificial chromosome PAC579 (D17S926 locus) mapped in the minimum LOH (loss of heterozygosity) deletion region of chromosome 17p13.3 in HCC. Four novel genes mapped in this genomic sequence area were isolated and cloned by wet-lab experiments, and the exons of these genes were located. 0–60 kb of this genomic sequence including the genes of interest was scanned with five different computational exon prediction programs as well as four splice site recognition programs. After analyzing and comparing the computationally predicted results with the wet-lab experiment results, some potential exons were predicted in the genomic sequence by using these programs.     

尖吻蝮蛇蛇毒出血毒素的纯化与部分性质

目的　被尖吻蝮蛇 （ Ｄｉｅｎａｇｋｉｓｔｒｏｄｏｎ ａｃｕｔｕｓ） 咬伤会引起严重的出血, 对蛇毒出血毒素的研究有利于治疗蛇伤出血药物筛选。 方法　采用 Ｓｅｐｈａｄｅｘ Ｇ７５, Ｄ Ｅ Ａ Ｅ Ｓｅｐｈａｄｅｘ Ａ５０, Ｓｅｐｈａｄｅｘ Ｇ２００ 和两次 Ｐ Ｂ Ｅ 聚焦层析纯化。 Ｓ Ｄ Ｓ Ｐ Ａ Ｇ Ｅ 电泳和等电聚焦电泳测定纯化样品的纯度和等电点。氨基酸组成用自动氨基酸分析仪测定。以小鼠背部皮下注射部位出血斑的面积来确定最小出血剂量和常规的方法测定酶活性。结果　从尖吻蝮蛇毒中纯化到一个相对分子量为５６ ０００ 的出血毒素 （ Ｄａ Ｈ Ｔ３）, 经氨基酸组成测定计算,它由 ４８７ 个氨基酸残基组成。此成分在 Ｓ Ｄ Ｓ Ｐ Ａ Ｇ Ｅ上显示出一条均一的蛋白染色带, 其ｐ Ｉ为５５０。该出血成分的最小出血剂量是 ２６μｇ, 具有蛋白水解酶活力, 其活力为 ３６８, 但没有精氨酯酶和磷脂酶 Ａ２ 活力。当加入 Ｅ Ｄ Ｔ Ａ 螯合剂去除金属离子后, 它们的出血活力和蛋白水解酶活力均丧失。 结论　这是从大陆尖吻蝮蛇毒中获得的一个新的出血金属蛋白酶 （ Ｄａ Ｈ Ｔ３）。     

On prediction of optical properties of two- and multiphase nanocomposites for nanomedicine

The theory of optical properties of nanoparticles is considered with the aid of dispersion relations, which are based on the Kramers-Kronig analysis. It is shown that one can utilize rather general dispersion relations, which hold for liquid matrices that contain nanoparticles. Wiener bounds incorporating the Kramers-Kronig analysis are utilized in assessment of the complex permittivity of a nanoparticle.     

Aromaticity and electronic properties of Heterosuperbenzene (Heterohexabenzocoronene)

A global electrophilicity parameter and the aromaticity of some heterocyclic polyaromatic hydrocarbons were evaluated on the basis of DFT calculations. The substitution of carbon atoms by nitrogen atoms dramatically changes the global electrophilicity of the molecules, with the fully substituted molecule being the most electrophilic with a reactivity very close to that of fullerene. Figure Fully substituted heterohexabenzocoronene Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Statistical analysis of the physical properties of the 20 naturally occurring amino acids

In order to describe the conformational and other physical properties of the 20 naturally occurring amino acid residues with a minimum number of parameters, several multivariate statistical analyses were applied to 188 of their physical properties and ten orthogonal properties (factors) were obtained for the 20 amino acids without losing the information contained in the original physical properties. The analysis consisted of three main steps. First, 72 of the physical properties were eliminated from further consideration because they did not pass statistical tests that they follow a normal distribution. Second, the remaining 116 physical properties of the amino acids were classified by a cluster analysis to eliminate duplications of highly correlated physical properties. This led to nine clusters, each of which was characterized by an average characteristic property, namely bulk, two hydrophobicity indices for free amino acids, one hydrophobicity index for amino acid residues in a protein, two types of -structure preference, -helix preference, and two types of bend-structure preference. The physical properties within a given cluster were highly correlated with each other, but the correlation between clusters was low. Third, a factor analysis was applied to the nine average classified properties and 16 additional physical properties to obtain a small number of orthogonal properties (ten factors). Four of these factors arise from the nine characteristic properties, and the remaining six factors were obtained from the 16 physical properties not included in the nine characteristic properties. Finally, most of the 188 physical properties could be expressed as a sum of these ten orthogonal factors, with appropriate weighting factors. Since these factors contain information relating almost all properties of all 20 amino acids, it is possible to estimate the numerical values of a property for one or two amino acids for which experimental data for this property are not available. For example, the estimated values for the Zimm-Bragg parameters at 20°C are 0.66 and 0.92 for proline and cysteine, respectively, computed from the first four factors.     

小兴安岭红松活立木树干腐朽与立地土壤理化特性的关系

活立木腐朽造成大量木材资源损失.研究活立木腐朽与立地生境之间的关系,对于科学合理地营林管理、减少木材资源损失有着积极的指导意义.2011年5月,使用阻抗仪对小兴安岭林区红松阔叶混交林中15株成熟龄的红松活立木树干根部腐朽状况及胸径进行了检测,同时分别在活立木根部、坡上距根部5 m和坡下距根部5 m处采集土样,测定土壤的含水率、容重、总孔隙度、pH值和有机质含量,并建立了活立木树干根部腐朽程度与其胸径和各样点土壤理化指标的回归方程.结果表明:成熟龄红松活立木树干根部腐朽程度与根部土壤5项理化指标有较强的相关性(R=0.687),且与土壤含水率呈显著正相关(R=0.507),而与坡上和坡下距根部5 m土壤各理化特性指标的相关性不显著.土壤含水率降至18.4％以下时将有助于降低树干根部的腐朽程度.成熟龄红松活立木树干根部腐朽程度与树龄的相关性不显著.