Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting <i>in vivo</i> stability of a protein from its primary sequence

Guruprasad, Kunchur; Reddy, Boojala Vijay B.; Pandit, M.W.

doi:10.1093/protein/4.2.155

Cited by 1,074 publications

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“…The instability index and grand average of hydropathicity (GRAVY) were estimated following the method of Guruprasad et al (1990) and Kyte and Doolittle (1982), respectively.…”

Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Amino Acid Sequences in Relation to Specificity and Physiochemical Properties of Some Microbial Nitrilases

Sharma¹,

Kushwaha²,

Sodhi³

et al. 2009

J Proteomics Bioinform

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In silico analysis of amino acid sequences of some aromatic and aliphatic microbial nitrilases for certain physiochemical properties and specificity to aromatic or aliphatic nitriles has been done. The multiple sequence alignment analysis of amino acid sequences has shown clear differences between aromatic and aliphatic nitrilases in terms of position specific presence of conserved amino acid. Statistical analysis of most of the physiochemical parameters did not show any clear distinction between the two nitrilases. In aromatic nitrilases the conserved amino acid residues besides active site domain triad (Glu, Lys, Cys) were His-129, Asn-168 and Arg-174 and these were replaced by Arg-129, His -168 and Lys-174 in aliphatic nitrilases. The physiochemical properties of these two groups of nitrilases also differed e.g. as compared to aliphatic nitrilases, aromatic nitrilases have lesser number of amino acid residues, lower molecular mass, higher pI values, higher content of Ala and Cys residues.

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“…The instability index and grand average of hydropathicity (GRAVY) were estimated following the method of Guruprasad et al (1990) and Kyte and Doolittle (1982), respectively.…”

Section: Methodsmentioning

confidence: 99%

In Silico Analysis of Amino Acid Sequences in Relation to Specificity and Physiochemical Properties of Some Microbial Nitrilases

Sharma¹,

Kushwaha²,

Sodhi³

et al. 2009

J Proteomics Bioinform

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“…The concentration of purified protein in the sample is evaluated from the value of extinction coefficient (Umang et al, 2012). The stability of protein is calculated from its instability index (II) and the proteins are predicted as stable when their instability index is smaller than 40; however when the value of instability index is greater than 40, the protein is regarded as unstable (Guruprasad et al, 1990). The volume occupied by aliphatic amino acids side chain (alanine, valine, leucine and isoleucine) relative to total volume occupied is called aliphatic index and it determines the thermostability of a globular protein (Walker, 2005).The hydrophilicity or hydrophobicity of protein is determined by grand average of hydropathicity (GRAVY), which is the ratio of sum of hydropathy values of all the amino acids to total number of residues in the sequence (Umang et al, 2012).…”

Section: Physicochemical Characterizationmentioning

confidence: 99%

In silico Characterization of Cellulases from Genus Bacillus

2017

IJCRR

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Background: Cellulases are hydrolytic enzymes which hydrolyze β-1,4-glycosidic linkage in cellulose and these are present in many microorganisms including bacteria, fungi and protozoa. The three types of cellulases involved in complete hydrolysis of cellulose are endoglucanase, exoglucanase and β-glucosidase. Various structural and functional domains are present in cellulases and among all these domains, cellulose binding and catalytic domains are found to be important for the hydrolysis of cellulose. Cellulases have showed promising applications in different industrial sectors like paper and pulp, textile, laundry, bioethanol production, brewing, detergent and waste management. A major focus has been given in the recent past by researchers to understand the functional domains and catalytic mechanism of this enzyme to make their effective use for industrial applications.

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“…Only the analysis of the instability index (II) showed a difference, and we found that ala310 had an II value of 39.08, suggesting that the protein is stable, and instead ser310 had a value of 40.26, suggesting protein instability. 12 To investigate the role of this polymorphism in schizophrenia we have analysed in a case-control association study the allele frequencies and the genotype distributions in a population of 99 schizophrenic patients and 116 unaffected controls. Allele frequencies, genotype distributions and the statistical analysis are shown in Table 1.…”

mentioning

confidence: 99%

Association between the ionotropic glutamate receptor kainate 3 (GRIK3) ser310ala polymorphism and schizophrenia

et al. 2002

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Schizophrenia is a severe psychiatric illness characterised by disturbance of thought, hallucination and delusions. 1 Several studies have suggested that dysfunctions in the glutamatergic transmission are linked to the pathogenesis of schizophrenia, and in particular an excessive activation of glutamate receptors seems to be related to the disruption of neuronal ionic gradients leading to excitotoxicity. 2-7 Numerous findings suggested that the kainate ionotropic glutamate receptors are primarily involved in this mechanism. Recently it has been demonstrated that the GRIK3 gene encoding for the ionotropic glutamate receptor kainate 3 contains a functional polymorphism (T928G) leading to the substitution of a serine with an alanine in position 310 of the protein sequence. [8][9][10][11] We performed an association study between the ser310ala GRIK3 polymorphism and schizophrenia in a sample of 99 schizophrenic patients and 116 controls. We found a significant difference in the genotype distribution and in particular considering the ala allele as dominant (P = 0.0105, odds ratio (OR) 2.031, 95% confidence interval (CI) 1.177-3.504). This finding suggests a potential role for GRIK3 for susceptibility to schizophrenia. Molecular Psychiatry (2002) 7, 416-418. DOI: 10.1038/ sj/mp/4000987Schizophrenia is a severe psychiatric illness characterised by disturbance of thought, hallucinations and delusions. Family, twin and adoption studies strongly evidenced genetic susceptibility and a pattern of inheritance belonging to the class of multifactorial complex disorders. 1 Many hypotheses have been made to explain the pathophysiology of schizophrenia and several studies suggest that dysfunctions in metabolism of neurotransmitters, such as dopamine, serotonin and glutamate, are directly implicated in the pathogenesis of this severe illness. A growing number of studies focused the attention on dysfunctions in glutamatergic pathway as a major susceptibility factor for schizophrenia. 2 Glutamate receptors are widely expressed in the central nervous system and play a fundamental role in synaptic plasticity and in all the processes underlying learning and memory. In particular the calcium influx through ionotropic glutamate receptors influences the regulation of transcriptional, translational and posttranslational processes fundamental for the function of brain cells. 3 One of the hypotheses about the molecular mechanisms leading to schizophrenia is the presence of an excessive activation of glutamate receptors. An increase in the basic metabolic activity along the glutamatergic axons has been demonstrated by PET scan studies in the cingulate cortex and hippocampal region of schizophrenic patients. 4,5 It has been hypothesised that this may cause a progressive excitotoxic cell death through the disruption of ionic gradients and the increase of intracellular calcium concentration. 6,7 Numerous findings suggested that ionotropic receptors of the kainate subtype, composed by the low affinity subunits GRIK1, GRIK2, GRIK3, and the high af...

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Correlation between stability of a protein and its dipeptide composition: a novel approach for predicting in vivo stability of a protein from its primary sequence

Cited by 1,074 publications

References 0 publications

In Silico Analysis of Amino Acid Sequences in Relation to Specificity and Physiochemical Properties of Some Microbial Nitrilases

In Silico Analysis of Amino Acid Sequences in Relation to Specificity and Physiochemical Properties of Some Microbial Nitrilases

In silico Characterization of Cellulases from Genus Bacillus

Association between the ionotropic glutamate receptor kainate 3 (GRIK3) ser310ala polymorphism and schizophrenia

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