Aliphatic index range 1) to 160. The index may be rega … In our case there are two classes: AVPs and non-AVPs. Also, the biochemical analysis indicated that the AKD9 is stable till 65 Jul 2, 2020 · The aliphatic index of the protein is defined as the relative volume occupied by aliphatic side chains, which include alanine, valine, isoleucine, and leucine, and contribute to protein thermostability . May 5, 2017 · The aliphatic index of a protein (volume of a protein filled by aliphatic side chains like isoleucine, alanine, valine and leucine) denotes the thermostability of globular proteins. Biochem Jul 1, 2014 · The aliphatic index for the hypothetical and conserved protein sequences involved in this study ranged from 71. Aliphatic index The aliphatic index of a protein is a measure of the relative volume occupied by aliphatic side chain of the following amino acids: alanine, valine, leucine and isoleucine. ProtParam module from BioPython. It may be regarded as a positive factor for the increase of thermostability of globular proteins. 5 to 9. Aliphatic index. 49 and 1. J. Aug 28, 2010 · Aliphatic index: 73. Isoelectric Point (pI) Isoelectric point (pI) is a pH at which an amino acid does not move in an electric field. A simple method for displaying the hydropathic character of a protein. 06. 1982). The aliphatic index of the HPs ranges from 73 (WP_148141124. 3). by aliphatic side chains (A, V, I and L), is regarded as a positive factor for the increase of thermal stability of globular proteins. The aliphatic index (AI) which is defined as the relative volume of a protein occupied by aliphatic side chain is regarded as the positive factor for the increase of thermal stability of globular proteins. Thermostability and aliphatic index of globular proteins. The instability index—The instability index provides Aug 28, 2020 · The instability index value for P18417 (47. Feb 3, 2014 · Ikai A. The computed aliphatic index for a given amino-acids sequence References. Extinction coefficient. Jan 4, 2024 · The aliphatic index was proposed by Ikai (1980) and evaluates the thermostability of proteins based on the percentage of each of the aliphatic amino acids that build up proteins. We also evaluated how strongly protein solubility is correlated with simple sequence features: aliphatic index (AI), fold index (FI), GRAVY index (GRAVY), and pI (pI). When compared to the bacterial enzyme, it shows a similar aliphatic index. Aliphatic index plays role in protein thermal stability. This family contains nitrilases that break carbon–nitrogen bonds and appear to be involved in the reduction of organic nitrogen compounds and ammonia production. Ikai (1980). The very low 4. 1 Petroleum Chemistry and The 43 genes belonging to the HSP40 gene family were sub-classified depending on domain conservation into types I, II and III. The aliphatic index AI is directly related to the mole fraction of Ala, Ile, Leu, and Val in the protein . Kyte J, Doolittle RF. Apr 19, 2021 · In this study are demonstrated several physicochemical characteristics of the cellulase enzyme. The AI of proteins from thermophilic bacteria was found to be significantly higher than that of ordinary proteins and hence, it can serve as a measure of thermostability of proteins . C. Acyclic aliphatic/non-aromatic compound Cyclic aliphatic/non-aromatic compound (cyclobutane)In organic chemistry, hydrocarbons (compounds composed solely of carbon and hydrogen) are divided into two classes: aromatic compounds and aliphatic compounds (/ ˌ æ l ɪ ˈ f æ t ɪ k /; G. The chromosomal distribution of MaSBP genes revealed that all genes are spread across ten out of the twelve chromosomes of M. The aliphatic index was proposed byIkai(1980) and evaluates the thermostability of proteins based on the percentage of each of the aliphatic amino acids that build up proteins. Considering a broader range of physicochemical properties can further improve and optimize the effectiveness and selectivity of AMPs against Staphylococcus aureus and other pathogens. Biochem. Isoelectric Point Predictions. The aliphatic index of a protein is calculated according to the following formula (Ikai, A. Aug 14, 2020 · Results revealed that activity of the Rhodococcus alkane-1-monooxygenase would be optimum in alkaline pH as their isoelectric points were in the range of 7. amrita. 1994. aleiphar, fat, oil). This means that its net charge becomes zero (zwitterion). The highest aliphatic Aliphatic index The aliphatic index of a protein is a measure of the relative volume occupied by aliphatic side chain of the following amino acids: alanine, valine, leucine and isoleucine. Aliphatic index = X(Ala) + a * X(Val) + b The high amount of aliphatic index shows the thermostability of protein over a wide temperature range (Rodr ıguez-Ruiz et al. The function instability_index(self) calculates the stability of proteins. It is found to span within a range References. The very high aliphatic index of all Ocimum proteins infers that these proteins may be stable for a wide range of temperature. 83°C (in method based on EPA Method 801. The aliphatic index of a protein is a measure of the relative volume occupied by aliphatic side chain of the following amino acids: alanine, valine, leucine and isoleucine. ties like protein length, amino acid composition, molecular weight, aliphatic index, extinction coefficient, isoelectric point, half-life, instability index and grand average of hydropathicity can be analyzed. The aliphatic index of a protein indicates a relative volume occupied by the aliphatic side chains (alanine, valine, isoleucine and leucine), which also increase the thermostability of the globular proteins with increasing value. 42) was found to be near 40 indicating that it was stable. aliphatic and aromatic compounds found in TPH is provided in Appendix D. Mar 1, 2021 · The instability index (II) was computed to be 31. Furthermore, all of these proteins are hydrophilic since they have a negative GRAVY score 61. Oct 1, 2021 · A high aliphatic index indicates that the protein is thermostable over a wide temperature range (Ikai, 1980). Proteins are dominated by random coils and alpha helixes. The mean and median values of The computed parameters include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY) . In these cases, a high aliphatic index alone cannot account for the differences in their thermostability. 3. Dec 1, 2024 · Aliphatic index, which measures the relative volume occupied by aliphatic side chains in a peptide or protein sequence [24], is crucial for correctly identifying HLA peptides. 12 (WP_041621668. 5 Modified which gives a measure of the aromatic and aliphatic content of the hydrocarbon in each of several carbon number ranges (fractions). 2k次，点赞14次，收藏16次。本文介绍了如何使用ExPASy官方网站的小程序来计算蛋白质的理化性质，如分子量、等电点等，无需复杂编程，只需输入氨基酸序列即可获取所需信息。 AA-Prop is a Protein Physicochemical Properties Prediction Tool. 1. With a high Aliphatic index proteins are more thermally stable. This one for “volatile” aliphatic and aromatic petroleum hydrocarbons (VPH) for gasoline range organics (GRO), and another for “extractable” aliphatic and aromatic petroleum hydrocarbons (EPH) for diesel range organics (DRO) and heavy fuel oils. The instability index values indicate that the proteins are highly stable. Very high aliphatic index of protein sequences indicates that protein may be stable for a wide temperature range. 54. 4. An increase in the aliphatic index increases the thermostability of globular proteins. Protein thermostability and hydrophobicity are also compared by GUD-VE. Aliphatic amino acids also are hydrophobic in nature. The aliphatic index of a protein is described as the relative volume occupied by the amino acids such as alanine, valine, isoleucine and leucine, which have an aliphatic side chain in their structure. Sequences that were correctly identified often had a relatively higher aliphatic index than negative sequences, indicating that sequences that were not sufficiently Mar 1, 2025 · These proteins' high aliphatic index implies that they are thermostable across a wide temperature range 60. 37%. 2018). The high aliphatic index indicates that these proteins can be stable at wide range of temperature [52, 53] . 58 to 79. 欢迎来到青岛农业大学于浩团队开放交流·合作共赢原创内容，欢迎转载，转载请注明出处主笔：于浩注意事项蛋白质的基本理化性质分析的方法很多，工具也很多，这里不可能一一列出。用ProtParam来进行分析比较简单，但是这里无法对多个蛋白进行分析。批量蛋白的基本理化性质可以用biopython工具 May 23, 2020 · 几个预测蛋白结构、理化性质的在线工具. 51. Automotive gasoline is a mixture of low-boiling hydrocarbon compounds Oct 2, 2018 · where n is the total number of amino acid pairs. Introduction to CLC Genomics Workbench. This is because the carbon ranges between the EPA RSL are similar to the carbon ranges in the TPHWG or the same indicator compound was used. See full list on vlab. The aliphatic index of a protein is calculated according to the following formula: Aliphatic index = X(Ala) + a * X(Val) + b * [X(Ile) + X(Leu)] where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction) of alanine, valine, isoleucine, and leucine. The Instability Index is calculated using the approach of Guruprasad et al. The relative volume of a protein occupied by its aliphatic side chains is termed as Aliphatic index (AI). 19%; CURS2, 89. H. (1989) Calculation of protein extinction coefficients from amino acid sequence data. 06 (OsTPP12), and Instability Index ranges were 28. A total of four HSP40 genes ( DNAJA1, DNAJA2, DNAJA3 and DNAJA4) ( Table 2) possessed the characteristic four canonical domains: J, Glycine-phenylalanine(G/F)-rich region, 2 zinc-finger like motifs, and the carboxyl-terminal (CTD), first observed in E coli. Jan 1, 2023 · The parameters are displayed in other sub-windows. 07 Grand average of hydropathicity (GRAVY): -0. 84 for AKD9 indicate its enhanced thermo-stability over a broad range of temperatures. Increase in thermostability of proteins is due the substitutions of amino acids: Gly to Ala, Ser to Thr, Lys to Arg, Asp to Glu, Met to Ala/Leu, Cys to Ile/Ala/Val Jul 9, 2024 · This property enables a plotting function, in which a scatter plot is provided for each individual aliphatic index score calculated. They usually range from − 2 to + 2 where the solubility of a protein in aqueous solutions decreases with the The aliphatic index of AhyMYBs ranged from 52. To optimize the performance a Naive Bayes classifier was trained with output values of a given method or a sequence feature. determined that the low aliphatic, medium aliphatic, and high aliphatic data in Table 2 are representative of GRO aliphatic, DRO aliphatic, and RRO aliphatic, respectively. Several studies have shown the presence and expression of PR genes in vari-ous plants including Arabidopsis thaliana and Oryza sativa The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). Value. We used visual data approaches for improved visualization so that the user can easily understand the parameter analysis. 30%; and CURS3, 86. 1982. , 1980). A high aliphatic index indicates that a protein is thermo-stable over a wide temperature range [20]. Therefore, a robust foundation for designing antimicrobial peptides can be established by considering hydrophobicity, instability index, and aliphatic index. It computes molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and GRAVY. Thus a high aliphatic index value seems to be a positive factor for increasing the thermo stability of globular proteins. Apr 19, 2024 · 文章浏览阅读2. In this study, the aliphatic indexes for the CC A statistical analysis shows that the aliphatic index, which is defined as the relative volume of a protein occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine), of proteins of thermophilic bacteria is significantly higher than that of ordinary proteins. The Aliphatic Index is the relative volume occupied by Alanine, Isoleucine, Leucine and Valine amino acids having aliphatic side chains (Bhattacharya et al. The instability index provides an estimate of the stability of one protein/peptide based on its amino acid composition [12,13]. 415 . A statistical analysis shows that the aliphatic index, which is defined as the relative volume of a protein occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine), of proteins of thermophilic bacteria is significantly higher than that of ordinary proteins. The Product manuals; Browse the manual. The high aliphatic index range 78. 88, 1895-1898 (1980) Thermostability and Atsushi Aliphatic Index of Globular Proteins IKAI Department of Biophysics The University of Tokyo, Received for publication, and Biochemistry, Hongo, Faculty Bunkyo-ku, September of Science, Tokyo 113 5, 1980 A statistical analysis shows that the aliphatic index, which is defined as the relative volume of a protein occupied by The Stability – Instability Index track estimates the stability of the protein in a test tube. Feb 26, 2021 · The National Center for Biomedical Ontology was founded as one of the National Centers for Biomedical Computing, supported by the NHGRI, the NHLBI, and the NIH Common Fund under grant U54-HG004028. Journal of molecular biology 157(1):105-132. 50, while the refractive index of aliphatic Texin® grades based on Desmodur® W is around 1. Also, the biochemical analysis indicated that the AKD9 is stable till 65 °C, which Dec 6, 2006 · WH: Wilkinson Harrison method. The aliphatic index and the grand average of hydropathicity (GRAVY) are used to compute this. Interestingly, the dataset's mean and median are around 89, demonstrating a significant tolerance to thermal fluctuations. 53–82. Contact information and citation COMMUNICATION J. 1980. 1). iv) Instability index: for calculating the instability index of input proteins, we used the Bio. This stability was reinforced by the aliphatic index, 86. acuminata. The aindex is defined as the relative volume occupied by aliphatic side chains (Alanine, Valine, Isoleucine, and Leucine). 6 万 Jul 9, 2019 · A protein whose instability index is <40 indicates stable and the value >40 infers unstable protein The lowest instability index observed for AtRbohD indicated its stability. Aliphatic Index ranges observed were 77. See Table 830-1 in WAC 173-340-900. Anal. (Table 1). Thus, aliphatic Desmopan® grades based on HDI exhibit refractive indexes between 1. 2019) and the negative values of GRAVY show the polar nature of the The aliphatic index was proposed by Ikai (1980) and evaluates the thermostability of proteins based on the percentage of each of the aliphatic amino acids that build up proteins. The higher the aliphatic index, the more stable is a protein in a broad range of temperatures. The aliphatic index (AI) which is defined as the relative volume of a protein occupied by aliphatic side chains (A, V, I, and L) is regarded as a positive factor for the increase of thermal stability of globular proteins. Table 1 %PDF-1. 77 (OsTPP3 Jan 16, 2013 · A comparative study of amino acid sequence and physicochemical properties indicates the affiliation of protein from the nitrilase/cyanide hydratase family. The decrease of Gini index in a tree model refers to the difference between the Gini index of a parent node and the weighted Gini index of its descending nodes. 1 b) indicate the range from -2 to +2 of proteins are positively related with the proteins being more hydrophobic (Kyteet al. 671 稳定不稳定又是怎么得出的，还有疏水性的打分怎么看，怎么样个数值才算比较疏水，多谢啊 最后编辑于 2022-10-09 · 浏览 4. Another measure for stability of proteins is the aliphatic index (AI) and increase in its value is reported to enhance the thermo stability of globular proteins [25]. Sep 2, 2022 · 相对分子质量 (KDa)、等电点(PI)、负电荷残基（Total number of negatively charged residues）、正电荷残基（Total number of positively charged residues）、不稳定系数(Instability index)、总平均亲水性(Grand average of hydropathicity-简写GRAVY)、脂肪指数(Aliphatic index) The aliphatic index of a protein is described as the relative volume occupied by the amino acids such as alanine, valine, isoleucine and leucine, which have an aliphatic side chain in their structure. This function calculates the Ikai (1980) aliphatic index of a protein. The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). 13 to 143. Furthermore, aliphatic index, signifying the relative volume of protein occupied by aliphatic side chains helps to study thermo stable properties of an enzyme. Aliphatic Index and Instability Index were also calculated. Aliphatic index = ( (Ala count) + a * (Val count) + b * (Ile count) + b * (Leu count) ) * 100 where a Aug 12, 2023 · 脂肪族指数（Aliphatic Index）：描述蛋白质中非极性氨基酸（如Ala、ILe等）的丰度和相对含量，用于评估蛋白质的溶解性和疏水性。 亲疏水性（GRAVY）：代表蛋白质分子中亲水性和疏水性氨基酸的 相对比例 ，该值越低表示蛋白质越疏水。 instability index, aliphatic index and grand average of hydropathicity (GRAVY) is also listed in the result page. The MADEP method is based on standard EPA methods, which allows it to be easily implemented by laboratories, though there are limitations with the method (see Section 3. They all have distinct substrate specificity and include nitrilase, cyanide In the best case, all data collected at the site would be aliphatic and aromatic carbon range fractions, but in reality, the analysis required for these data is relatively expensive and more complex, and there is almost always a need (by responsible parties and state tank funds) to use a less-expensive bulk hydrocarbon carbon range TPH analysis Dec 1, 2018 · Whereas, the Aliphatic Index (AI) acts as a positive factor for thermostability of protein molecules and shaping the recent observations it support that 1GZI protein has maximum stability in increasing or decreasing the water temperature range. Jan 1, 2025 · In allantoinase dataset, the aliphatic index ranges from 82 to 102. A protein/peptide whose instability index is smaller than 40 is predicted as stable. AA-Prop is a Protein Physicochemical Properties Prediction Tool. 3. SeqUtils. Journal of Biochemistry 88(6):1895-1898. edu The aliphatic index of a protein is calculated according to the following formula: Aliphatic index = X(Ala) + a * X(Val) + b * [X(Ile) + X(Leu)] where X(Ala), X(Val), X(Ile), and X(Leu) are mole percent (100 X mole fraction) of alanine, valine, isoleucine, and leucine. Aliphatic index 脂溶指数: XXXX 小于100比较亲水 Grand average of hydropathicity 亲水性平均值 (GRAVY): XXXX 定义为序列中所有氨基酸亲水值的总和与氨基酸数量的比值，负值越大表示亲水性越好好，正值越大表示疏水性越强。 Feb 15, 2021 · The aliphatic index of a protein is defined as the relative volume constituted by aliphatic side chains (alanine, valine, isoleucine, and leucine) and a relatively high aliphatic index can be considered a positive factor for increased stability at a relatively wider range of temperatures [19]. Automotive Gasoline. May 29, 2024 · The aliphatic index was proposed by Ikai (1980) and evaluates the thermostability of proteins based on the percentage of each of the aliphatic amino acids that build up proteins. Bjellqvist B, Basse B, Olsen E, Celis JE. 26°C (in AhyMYB63) to 92. Ecology is in the process of accrediting laboratories for the Physical and chemical properties of petroleum constituents, TPH carbon ranges (fractions), and metabolites Properties of aliphatic and aromatic hydrocarbon fractions Alterations of petroleum mixtures in the environment through weathering processes Definition of “TPH” in environmental media in risk assessment 4. Apr 8, 2024 · In the current investigation, a total of 42 full-length, non-redundant small heat shock proteins (sHsp) were detected in Cyprinus carpio, Labeo rohita, Danio rerio, Salmo salar, Oncorhynchus mykiss, and Clupea harengus. Gill, S. The aliphatic index was higher than 71 providing information that the proteins are highly thermostable. and von Hippel, P. Oct 1, 2021 · The higher aliphatic index of DomCDRs (Figure 2B) indicated that they contain more aliphatic side chains and are more stable . All the sHsps were shown to have higher aliphatic index values, which is an indication that The use of aliphatic isocyanates lowers the refractive index of TPU. 24, which classifies the multi-epitope vaccine as a stable molecule. 4 %âãÏÓ 16 0 obj > endobj xref 16 41 0000000016 00000 n 0000001391 00000 n 0000001490 00000 n 0000002019 00000 n 0000002190 00000 n 0000002301 00000 n 0000002414 00000 n 0000003401 00000 n 0000004254 00000 n 0000004948 00000 n 0000006106 00000 n 0000007234 00000 n 0000008368 00000 n 0000008504 00000 n 0000008951 00000 n 0000009341 00000 n 0000009376 00000 n 0000009401 00000 n Aliphatic index It has been suggested that the aliphatic amino acids (A, I, L and V) are responsible for the thermal stability of proteins. Jul 18, 2016 · In addition, the aliphatic index had a range of 57. 06 and the grand average of hydropathicity ranged from −0. The index is calculated by the following formula. 预测理化性质：分子量(Da)、等电点(PI)\不稳定系数(Instability index)、亲水指数(Grand average of hydropathicity-简写GRAVY)、脂溶指数(Aliphatic index) A high aliphatic index indicates that the protein is thermostable over a wide temperature range . The distances d, between 3 and 10 Å, were divided into 35 bins of 0. 96 for the serine proteases and 79. 2 Å width; the last bin contains all distances larger than 10 Å. The aliphatic index of a protein is defined as the relative volume occupied by aliphatic side chains (alanine, valine, isoleucine, and leucine). Higher aliphatic index (87 to 95) indicated that these enzymes are thermostable. 903 to −0. . The pH of the The GRAVY values ( Fig. , 1990,, which predicts regional instability by calculating the weighted sum of dipeptides that occur more frequently in unstable proteins when compared to stable proteins. The Gini index ranges from 0 to 1 and the index is closer to 0 if the sample is purer. 14 (OsTPP4) to 94. The predicted aliphatic index of CURS1 protein was 99. There are proteins with high aliphatic index values regardless of the origin. The sHsp genes were classified into three groups based on phylogenetic analysis. Further information on whole petroleum products, their identity, major components, and physical/chemical properties is found in Appendix E. ipeqh rjozk grp qhxkn dhqsnk lfpk fxnekc btxzuf mws uhsx gxybh khon wvsp ngmcsc fwct