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... algorithms suitable for each type (Abagyan & Maiorov, 1988; Mitchell et al., 1989; Sali & Blundell, 1989; Taylor & Orengo, 1989; Vriend & Sander, 1991; Alexandrov et al., 1992; Fischer et al., 1992; =-=Holm & Sander, 1993-=-a). Based on the observed similarities among 3-dimensional structures, proteins have been classified into structural families (Levitt & Chothia, 1976; Richardson, 1981; Chothia & Finkel" . Downloaded ...

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...ilies of globular proteins methods: minimal spanning trees and hierarchical trees based on agglomerative clustering. All protein coordinates were obtained from the Brookhaven Protein Data Bank (PDB) (=-=Bernstein et al., 1977-=-; Abola et al., 1987). The set of 158 protein structures was derived from Appendix 3 of Protein Architecture (Lesk, 1991). Table 1 lists the proteins and their PDB filenames. Pairwise tests Finding se...

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...hown that positions after superposition. RMS is a useful distance proteins fall into families of related structures (Levitt & metric for comparing structures that are nearly identical: Chothia, 1976; =-=Richardson, 1981-=-; Richardson & Richard- for example, when refining or comparing structures obson, 1989; Chothia & Finkelstein, 1990). How many fam- tained from X-ray crystallography or NMR experiments. ilies are ther...

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...formational deviations. If two structures are not in the measures of structural similarity have been developed same energy well, or if errors are large, RMS will lose its (Remington & Matthews, 1978; =-=Taylor & Orengo, 1989-=-; underlying justification. In addition, the use of an RMS Rackovsky, 1990; Sali & Blundell, 1990). There is no un- distance criterion to compare two protein structures rederlying fundamental principl...

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...ov, Laboratory of the Mathematical Biology, Building 469, Room 151, FCRF-NCI, Frederick, Maryland 21702; e-mail: nicka@ncifcrf.gov. 866 stein, 1990; Overington et al., 1990; Rackovsky, 1990; Murzin & =-=Chothia, 1992-=-; Pascarella & Argos, 1992; Holm & Sander, 1993b; Orengo et al., 1993; Yee & Dill, 1993). From the results of comparison of 3-dimensional structures and of amino acid sequences, Chothia (1992) estimat...

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... 1991; Alexandrov et al., 1992; Fischer et al., 1992; Holm & Sander, 1993a). Based on the observed similarities among 3-dimensional structures, proteins have been classified into structural families (=-=Levitt & Chothia, 1976-=-; Richardson, 1981; Chothia & Finkel" . Downloaded from www.proteinscience.org on January 30, 2008 - Published by Cold Spring Harbor Laboratory Press Reprint requests to: Nickolai Alexandrov, Laborato...

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...een developed same energy well, or if errors are large, RMS will lose its (Remington & Matthews, 1978; Taylor & Orengo, 1989; underlying justification. In addition, the use of an RMS Rackovsky, 1990; =-=Sali & Blundell, 1990-=-). There is no un- distance criterion to compare two protein structures rederlying fundamental principle dictating that one similar- quires making assignments in which atom i of protein 1 ity measure ...

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...occurred. A 2D I5N-'H HSQC spectrum (Bax et al., 1990b; Nonvood et al., 1990) and all 3D experiments for the backbone assignment were recorded on a single HzO sample. HNCO and HNCA (Kay et al., 1990; =-=Grzesiek & Bax, 1992-=-a). HN(C0)CA (Bax & Ikura, 1991; Grzesiek & Bax, 1992a). HN(CA)CO (Clubb et al., 19924, HN(COCA)HA(Kay et al., 1992), HN(CA)HA(Clubbet al., 1992b; Kay et al., 1992). CBCA(C0)NH (Grzesiek & Bax, 1992b)...

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...wo structures only ferent families? If so, they are tightly knit. What can we if the individual errors are Gaussian-distributed with zero learn about the forces of protein folding and evolution mean (=-=Beers, 1957-=-). The Gaussian distribution assumpfrom observing how proteins cluster into families? tion can be reframed as an assumption that the differIn order to address these questions, it is necessary to ences...

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....sNMR of cutinase Side-chain assignments Downloaded from www.proteinscience.org on April 14, 2008 - Published by Cold Spring Harbor Laboratory Press Aliphatic side-chain resonances The "N TOCSY-HMQC (=-=Marion et al., 1989-=-a) experiment proved to be too insensitive for the uniformly "C, "N-labeled cutinase sample. Therefore, the assignment of the aliphatic sidechain resonances was based on 3D CCH- and H(C)CH-TOCSY exper...

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...ypes of structural similarity have been detected by means of different algorithms suitable for each type (Abagyan & Maiorov, 1988; Mitchell et al., 1989; Sali & Blundell, 1989; Taylor & Orengo, 1989; =-=Vriend & Sander, 1991-=-; Alexandrov et al., 1992; Fischer et al., 1992; Holm & Sander, 1993a). Based on the observed similarities among 3-dimensional structures, proteins have been classified into structural families (Levit...

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...ura, 1991; Grzesiek & Bax, 1992a). HN(CA)CO (Clubb et al., 19924, HN(COCA)HA(Kay et al., 1992), HN(CA)HA(Clubbet al., 1992b; Kay et al., 1992). CBCA(C0)NH (Grzesiek & Bax, 1992b), and HBHA(CBCAC0)NH (=-=Grzesiek & Bax, 1993-=-) spectra were recorded with minor modifications as described below. The HN(C0CA)HA and HN(CA)HA experiments were performed as modified 3D versions (no C" frequency labeling) of the 4D experiments pub...

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...of the Mathematical Biology, Building 469, Room 151, FCRF-NCI, Frederick, Maryland 21702; e-mail: nicka@ncifcrf.gov. 866 stein, 1990; Overington et al., 1990; Rackovsky, 1990; Murzin & Chothia, 1992; =-=Pascarella & Argos, 1992-=-; Holm & Sander, 1993b; Orengo et al., 1993; Yee & Dill, 1993). From the results of comparison of 3-dimensional structures and of amino acid sequences, Chothia (1992) estimated the total number of pos...

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... structures (Levitt & metric for comparing structures that are nearly identical: Chothia, 1976; Richardson, 1981; Richardson & Richard- for example, when refining or comparing structures obson, 1989; =-=Chothia & Finkelstein, 1990-=-). How many fam- tained from X-ray crystallography or NMR experiments. ilies are there? Are the families “tightly knit” or “loosely However, RMS is of limited value as a general measure knit”? That is...

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...occurred. A 2D I5N-'H HSQC spectrum (Bax et al., 1990b; Nonvood et al., 1990) and all 3D experiments for the backbone assignment were recorded on a single HzO sample. HNCO and HNCA (Kay et al., 1990; =-=Grzesiek & Bax, 1992-=-a). HN(C0)CA (Bax & Ikura, 1991; Grzesiek & Bax, 1992a). HN(CA)CO (Clubb et al., 19924, HN(COCA)HA(Kay et al., 1992), HN(CA)HA(Clubbet al., 1992b; Kay et al., 1992). CBCA(C0)NH (Grzesiek & Bax, 1992b)...

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...if. In addition, galactose binding protein scores well for the presence of a calcium binding loop. Consistent with this finding, galactose binding protein was reported to have a calcium binding site (=-=Vyas et al., 1987-=-) that resembles the EF hand without the helices. T4 lysozyme, which scored 5th for the presence of an EF hand, scores 69th for the presence of the calcium binding loop. Although T4 lysozyme has two h...

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...pid layer, a significant rearrangement of this flap increases the hydrophobic surface at the lipid-binding region, improving adsorption and allowing binding of the substrate (Brzozowski et al., 1991; =-=Derewenda et al., 1992-=-; van Tilbeurgh et al., 1993). E solanipisi cutinase does not possess a pronounced flap region covering the active site (Martinez et al., Reprint requests to: Henri A.M. Pepermans, Unilever Research L...

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...rdinates were obtained from the Brookhaven Protein Data Bank (PDB) (Bernstein et al., 1977; Abola et al., 1987). The set of 158 protein structures was derived from Appendix 3 of Protein Architecture (=-=Lesk, 1991-=-). Table 1 lists the proteins and their PDB filenames. Pairwise tests Finding sequence alignments To first choose a few examples, it is reasonable to believe that sperm whale myoglobin (lmbd) and the ...

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... algorithms suitable for each type (Abagyan & Maiorov, 1988; Mitchell et al., 1989; Sali & Blundell, 1989; Taylor & Orengo, 1989; Vriend & Sander, 1991; Alexandrov et al., 1992; Fischer et al., 1992; =-=Holm & Sander, 1993-=-a). Based on the observed similarities among 3-dimensional structures, proteins have been classified into structural families (Levitt & Chothia, 1976; Richardson, 1981; Chothia & Finkel" . Downloaded ...

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...rd place is occupied by common SARF from poliovirus (2plv) and tomato bushy stunt virus (2tbv). The similarity in these top 3 cases has already been discussed in the literature (Lebioda & Stec, 1988; =-=Huber et al., 1987-=-; Hogle et al., 1985). The similarity between bacteriochlorophyll-A (3bcl) and pea lectin (21tn) is just a large 0-sheet, formed by 8 strands. However, this is an interesting example because it consis...

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...ests to: Nickolai Alexandrov, Laboratory of the Mathematical Biology, Building 469, Room 151, FCRF-NCI, Frederick, Maryland 21702; e-mail: nicka@ncifcrf.gov. 866 stein, 1990; Overington et al., 1990; =-=Rackovsky, 1990-=-; Murzin & Chothia, 1992; Pascarella & Argos, 1992; Holm & Sander, 1993b; Orengo et al., 1993; Yee & Dill, 1993). From the results of comparison of 3-dimensional structures and of amino acid sequences...

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...gree of similarity. Several formational deviations. If two structures are not in the measures of structural similarity have been developed same energy well, or if errors are large, RMS will lose its (=-=Remington & Matthews, 1978-=-; Taylor & Orengo, 1989; underlying justification. In addition, the use of an RMS Rackovsky, 1990; Sali & Blundell, 1990). There is no un- distance criterion to compare two protein structures rederlyi...

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...ng protein (lbbp). Third place is occupied by common SARF from poliovirus (2plv) and tomato bushy stunt virus (2tbv). The similarity in these top 3 cases has already been discussed in the literature (=-=Lebioda & Stec, 1988-=-; Huber et al., 1987; Hogle et al., 1985). The similarity between bacteriochlorophyll-A (3bcl) and pea lectin (21tn) is just a large 0-sheet, formed by 8 strands. However, this is an interesting examp...

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... 434 Cro, 434 repressor, trp repressor, and catabolite gene activator protein (CAP) all have sequence similarity in a region of 22 amino acids, corresponding to the helix-turn-helix structural motif (=-=Ohlendorf et al., 1983-=-). How widely distributed is the helix-turn-helix motif throughout the protein database? We use CONGENEAL to search the dataset for the helixturn-helix conformation. In our search, the helix-turnhelix...

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...rminal side of the central P-sheet by holding these two strands together. The alignment of the sequence of E sohi pin' cutinase to seven other cutinases (Ettinger et al., 1987: Sweigard et al., 1992; =-=Ohnishi et al., 1995-=-) shows that E solnni pisi cutinase is the only cutinase so far with this type of amide-aromatic interaction. In six other cutinases, the Trp at position 69 is conserved, but a Pro rather than an Ala ...

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...e are 43 substitutions in the other 103 Fob KOL (light chain) Immunoglobulin Vx domain 2fo4-1 2rhe 0.079 residues. Despite these sequence differences, the structures are found to be nearly identical (=-=Matthews, 1985-=-). Other Ribonuclease A Ribonuclease S 3rn3 lrns 0.103 sets of proteins that are found to be highly similar by CONGENEAL include DNA binding proteins (434 Cro, Ribonuclease A Ribonuclease S 7rsa lrns ...

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...helices. The catalytic apparatus of cutinase is composed of the catalytic triad SerIz0, HisIs8, and Asp"', an oxyanion binding site (main-chain nitrogens of Ser4' and Gin'*' and the 07 atom of Ser4'; =-=Martinez et al., 1994-=-), and other binding determinants further away from the scissile ester bond of the substrate. NMR spectroscopy can provide additional information, not obtained using X-ray diffraction, that is importa...

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...ijden et al., 1994). Motional aspects of structure-function relations, such as conformational changes, internal motions, kinetics, and folding, are subjects well suited for study by NMR spectroscopy (=-=Bax, 1991-=-; Bax & Grzesiek, 1993). Here we present nearly complete 'H, "C, and "N backbone and side-chain assignments of E soluni pisi cutinase using 3D NMR techniques. Analysis of amide hydrogen exchange data,...

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...nal. Instead, water suppression was typically done by applying a proton spin-lock pulse (Messerle et al., 1989) after the first INEPT transfer. A slightly modified version of the 3D COCAH experiment (=-=Dijkstra et al., 1994-=-) was recorded on the H20 sample, to prevent interpretation problems due to deuterium isotope shifts and variation in sample conditions (Remerowski et al., 1994; Zhang & Gmeiner, 1996), as well as on ...

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...ment with a 75-ms mixing time. Although there might be a slight degree of spindiffusion at this mixing time for a protein of this size, this does not prevent the determination of secondary structure (=-=Grzesiek et al., 1992-=-). The interpretation of the sequential NOE data was hindered by overlap in the 3D NOESY-HSQC spectrum. However, the information obtained from this spectrum was sufficient for a secNH exch. daN(1-1, I...

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...xample of this limitation is in the comparison of a/p barrels such as triose phosphate isomerase (TIM). It has been suggested that all the known a//3 barrels may have diverged from a common ancestor (=-=Farber & Petsko, 1990-=-). If so, and if the process of evolutionary divergence involves changing loop lengths while retaining secondary structural domains, then evolutionary “distance” requires a similarity measure that car...

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...lar to previously noted by Richardson and Richardson (1988). the parvalbumin EF hand. Interestingly, the N-terminal They found that cytochrome c peroxidase and ribosomal EF hands do not bind calcium (=-=Satyshur et al., 1988-=-). L7/L12 protein contain conformations similar to the DNA The method correctly identifies bovine intestinal calbinding helix pairs in gene activator and repressor pro- cium binding protein as being s...

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...equency labeling in the HNCO-type experiments was eliminated by two 180" I3Ca pulses applied at the midpoints of both parts of the "N constant-time evolution time, before and after the 180" "N pulse (=-=Grzesiek et al., 1993-=-). Evolution under the lJN.co coupling during I5N frequency labeling in the HNCA-type experiments was eliminated in a similar manner. None of the experiments described above used presaturation of the ...

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...on on minimal medium. Briefly, uniformly 'IC, I5N-labeled cutinase, preceded by a IS-residue propeptide, was obtained by growing E. coli strain WK6, containing the plasmid CTI, at 30°C on M9P medium (=-=Sambrook et al., 1989-=-) with 1 mg/L thiamine, containing [ "CID-glucose (98% 'jC. fermentation grade, Cambridge Isotope Laboratories) and "NH4CI (99% I5N. Cambridge Isotope Laboratones) as the sole carbon and nitrogen sour...

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...x method (Wishart et al., 1992; Wishart & Sykes, 1994) was applied to cutinase, using the random coil values determined by Wishart et al. (1995). The empirical correlation of backbone 4 and $ values (=-=Spera & Bax, 1991-=-) was used to predict C" and Cp secondary chemical shifts from the crystal structure of cutinase (ICUS; Martinez et al., 1992). Supplementary material in Electronic Appendix Table 1 lists the 'H, "C, ...