Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences

Lemesle-Varloot, L.; Henrissat, Bernard; Gaboriaud, Christine; Bissery, V.; Morgat, Anne; Mornon, Jean‐Paul

doi:10.1016/0300-9084(90)90120-6

Cited by 281 publications

(206 citation statements)

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“…The significant differences in the numbers and locations of the hydrophobic residues in the P. abyssi and E. coli proteins (Table 1 and Fig. 4) were analyzed by the HCA method (20,38). The results are shown in Fig.…”

Section: Resultsmentioning

confidence: 99%

“…Secondary structure was predicted by using the PHDsec program from the PredictProtein server (61)(62)(63), and multiple alignments were performed by using the MaxHom.SSP program from the same server (64). The Hydrophobic Cluster Analysis (HCA) program was used for analysis of hydrophobic clusters (20,38). Modeling of the tridimensional structure was performed by amino acid replacement and energy minimization with the Swiss-Model program of the ExPaSy server (55,56) and the Insight II and Homology programs (Biosym Technologies Co.).…”

Section: Methodsmentioning

confidence: 99%

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Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli

et al. 1997

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The genes coding for aspartate transcarbamylase (ATCase) in the deep-sea hyperthermophilic archaeon Pyrococcus abyssi were cloned by complementation of a pyrB Escherichia coli mutant. The sequence revealed the existence of a pyrBI operon, coding for a catalytic chain and a regulatory chain, as in Enterobacteriaceae.Comparison of primary sequences of the polypeptides encoded by the pyrB and pyrI genes with those of homologous eubacterial and eukaryotic chains showed a high degree of conservation of the residues which in E. coli ATCase are involved in catalysis and allosteric regulation. The regulatory chain shows more-extensive divergence with respect to that of E. coli and other Enterobacteriaceae than the catalytic chain. Several substitutions suggest the existence in P. abyssi ATCase of additional hydrophobic interactions and ionic bonds which are probably involved in protein stabilization at high temperatures. The catalytic chain presents a secondary structure similar to that of the E. coli enzyme. Modeling of the tridimensional structure of this chain provides a folding close to that of the E. coli protein in spite of several significant differences. Conservation of numerous pairs of residues involved in the interfaces between different chains or subunits in E. coli ATCase suggests that the P. abyssi enzyme has a quaternary structure similar to that of the E. coli enzyme. P. abyssi ATCase expressed in transgenic E. coli cells exhibited reduced cooperativity for aspartate binding and sensitivity to allosteric effectors, as well as a decreased thermostability and barostability, suggesting that in P. abyssi cells this enzyme is further stabilized through its association with other cellular components.Studies of extremophilic organisms provide information on the molecular mechanisms of biological adaptation to extreme environments. In this regard, Pyrococcus abyssi is of particular interest, being a hyperthermophilic and barophilic/barotolerant archaeon. This euryarchaebacterium, isolated from a deepsea hydrothermal vent located 2,000 m deep in the North Fiji Basin, was characterized by Erauso et al. (15,16). It is a heterotrophic and strictly anaerobic microorganism and belongs to the sulfur-metabolizing group. At atmospheric pressure, it grows at 67 to 102°C, with an optimum at 96°C. Hydrostatic pressure slightly increases the growth rate of P. abyssi as well as its optimal and maximal growth temperatures (16).Aspartate transcarbamylase (ATCase) (EC 2.1.3.2) is the first enzyme of the pyrimidine biosynthetic pathway. It catalyzes the carbamylation of the amino group of aspartate by carbamylphosphate with formation of carbamylaspartate and phosphate. ATCase is extensively studied as a model for structure-function relationships in cooperativity and allosteric regulation mechanisms, as well as for the evolution of these mechanisms from prokaryotes to humans. The structure and properties of the Escherichia coli enzyme have been studied in detail (for reviews, see references 3, 10, 26, 32, 40, and 70).This dodecame...

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli

et al. 1997

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“…The new encoding scheme can be derived in the 3-, 2-, or 1-dimensional form [19]. Finally, hydrophobic cluster analysis (HCA) analysis constitutes another well-known technique for the 2D representation of protein sequences [20][21][22][23]. Randić et al ultimately approached protein representations by using 2D schemes based on nucleotide triplet codons or virtual genetic code [24,25].…”

Section: Introductionmentioning

confidence: 99%

Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L.

et al. 2006

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The development of 2D graph-theoretic representations for DNA sequences was very important for qualitative and quantitative comparison of sequences. Calculation of numeric features for these representations is useful for DNA-QSAR studies. Most of all graph-theoretic representations identify each one of the four bases with a unitary walk in one axe direction in the 2D space. In the case of proteins, twenty amino acids instead of four bases have to be considered. This fact has limited the introduction of useful 2D Cartesian representations and the corresponding sequences descriptors to encode protein sequence information. In this study, we overcome this problem grouping amino acids into four groups: acid, basic, polar and non-polar amino acids. The identification of each group with one of the four axis directions determines a novel 2D representation and numeric descriptors for proteins sequences. Afterwards, a Markov model has been used to calculate new numeric descriptors of the protein sequence. These descriptors are called herein the sequence 2D coupling numbers (f k ). In this work, we calculated the f k values for 108 sequences of different polygalacturonases (PGs) and for 100 sequences of other proteins. A Linear Discriminant Analysis model derived here (PG = 5.36 AE f 1 À 3.98 AE f 3 À 42.21) successfully discriminates between PGs and other proteins. The model correctly classified 100% of a subset of 81 PGs and 75 non-PG proteins sequences used to train the model. The model also correctly classified 51 out of 52 (98.07%) of proteins sequences used as external validation series. The uses of different group of amino acids and/or axes orientation give different results, so it is suggested to be explored for other databases. Finally, to illustrates the use of the model we report the isolation and prediction of the PG action for a novel sequence (AY908988) isolated by our group from Psidium guajava L. This prediction coincides very well with sequence alignment results found by the BLAST methodology. These findings illustrate the possibilities of the sequence descriptors derived for this novel 2D sequence representation in proteins sequence QSAR studies.

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“…No definite window was used. Highly hydrophobic (VILF) or moderately hydrophobic (WMY) residues tend to form clusters of various shapes and sizes [23]. Clusters of similar shapes, sizes and relative positions express similar patterns in polypeptide folding of the protein.…”

Section: Methodsmentioning

confidence: 99%

Two identical hydrophobic clusters are present on the same actin monomer: interaction between one myosin subfragment‐1 and two actin monomers

Labbé¹,

Boyer²,

Benyamin³

1995

FEBS Letters

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Two-dimensional hydrophobic clusters analysis (IICA) was used to compare the distribution of hydrophobic clusters along various actin sequence. HCA-deduced patterns were not altered by amino-acid variations throughout the evolution of actin and we observed similar hydrophobic motifs comprising myosin subfragment-I ATP-independent binding sites. HCA suggested the presence of two groups of identical hydrophobic motifs (A~ and A2) which bound on each side of the S1 (63 kDa-31 kDa) connecting segment in relation with two actin monomers. This connection is important in communications between actin-and nucleotide-binding sites. We postulate that some relation and message between the two motifs A~ and A 2 take place through myosin subfragment-I (63 kDa-31 kDa) connecting segment.1~ ey words'," Acto-myosin; Hydrophobic cluster; Structure comparison 1~ IntroductionIdentification of the actin-myosin interface is essential in t nderstanding the cyclical enzymatic and mechanical process c f myofibrillar contraction.Atomic resolution of the actin structure [1,2] and the threeciimensional atomic model of F-actin decorated with rabbit ~aymotryptic-S1 [3] or Dictyostelium myosin S1 [4] revealed I ~cations of the myosin head on F-actin. This molecular model f the actin-myosin complex derived from the X-ray structure l zveals a close contact between a myosin subfragment-I and 1 ~o actin monomers. A first contact includes carboxyl residues ,2, 3, 4, 24, 25, 99 and 100. In a second contact, exposed actin 1 ydrophobic residues 144, 341,345,349 and 352 are concerned. "he third contact involves proline residues (332-333) of actin. ~11 of these contacts involve a single monomer. A second mon-~,mer is close to the myosin heavy chain and the interaction i ~cludes the cz-helix formed by actin residues Trp79 to Asn92 flat formed a weak binding contact and was cross-linked [5,6].The Taylor-Amos model [7] of acto-S1 suggests that S1 has n extensive contact with an actin monomer (acl) and a weaker ,. ontact with an adjacent actin monomer (ac2); and two differ-,, nt rigor complexes were suggested [8,9], with SI binding to :-actin occurring in two steps with actin monomers. Using .,uccessively EDC and DMS, we previously cross-linked two lnonomers to 20-kDa and 50-kDa skeletal S1 fragments, re-: Corresponding author. Fax: (33) (67) 60 94 78.spectively [10], and in vitro studies showed that subfragment-I alone can produce the sliding movement of the actin filament [111.Chemical cross-linking [12], NMR [13,14] and immunochemical studies [15,16,[17][18][19][20] have pinpointed actin segments in subdomain-1, residues 1 28, 96-103, 112-125, 338 348 and 360-372 which are able to bind with the myosin head.Furthermore, the (27 kDa-50 kDa-20 kDa) trypsin split myosin subfragment-1, which could no longer be activated by actin, did not bind to the two sites located in the 96-125 region, but it still interacted with the 338-348 and 360--372 segments [191. The presence of hydrophobic interactions in the actin myosin complex have already been sugge...

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Hydrophobic cluster analysis: procedures to derive structural and functional information from 2-D-representation of protein sequences

Cited by 281 publications

References 51 publications

Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli

Aspartate transcarbamylase from the deep-sea hyperthermophilic archaeon Pyrococcus abyssi: genetic organization, structure, and expression in Escherichia coli

Novel 2D maps and coupling numbers for protein sequences. The first QSAR study of polygalacturonases; isolation and prediction of a novel sequence from Psidium guajava L.

Two identical hydrophobic clusters are present on the same actin monomer: interaction between one myosin subfragment‐1 and two actin monomers

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