Recurrence of the cytochrome fold in a nitrate-respiring bacterium

Assessment of secondary-structure prediction of proteins. Comparison of computerized Chou-Fasman method with others

A method predicting protein secondary structure from sequence information could be assessed for its real efficiency by applying it to a number of proteins which lie completely outside a given data set. This type of test is performed for the three methods of Chou and Fasman (Adv. Enzymol. 47 (1978) 45-148), Robson and co-workers (J. Mol. Biol. 120 (1978) 97-120) and Lim (J. Mol. Biol. 88 (1974) 873-894) by using data of 19 proteins for the former two methods and 11 proteins for the method of Lim. The prediction abilities of these methods turn out to be of almost the same level, but unexpectedly low: their average scores are commonly less than 55% measured by the three-state assessment (alpha, beta and coil) or less than 45% measured by the four-state assessment (alpha, beta, turn and coil). This level of accuracy is more than 20% lower than that of current expectations as summarized by Schulz and Schirmer (Principles of Protein Structure (1979) Ch. 6, Springer, New York). A joint prediction attempted with the simultaneous usage of the three prediction methods did not improve the results. Causes and implications of the unsatisfactory results are discussed. In this study, computer programs were prepared for the methods of Chou and Fasman and of Robson and co-workers. While difficulties arose in the course of the computerization of the Chou-Fasman method, the prediction algorithm was arranged in a fully automatic form with optimization of the original rules as well as introduction of a modified treatment for solving the overlap among initially predicted regions of the secondary structures. Large discrepancies observed between the original results and those obtained by the computerized method are examined.

Conformational energy refinement of horse-heart ferricytochrome c

The reported X-ray structure of horse-heart ferricytochrome c has been refined by conformational energy calculations, using a three-stage computational procedure. In stage I, the atomic positions are adjusted to conform to idealized bond lengths and bond angles characteristic of small amino acid derivatives, while yet remaining as close as possible to the X-ray coordinates. In stage II, atomic overlaps are eliminated by adjusting the backbone and side-chain dihedral angles to minimize the nonbonded energy, hydrogen-bonded energy, and rotational energy contributions. In the final stage of refinement, the electrostatic energy and a more accurate hydrogen-bonded energy treatment are considered, in addition to the energy contributions of stage II. A "fitting potential" of gradually decreasing strength is imposed in both stages II and III, in order to keep the computed structure as similar to the x-ray structure as is consistent with a low-energy conformation. The final computed structure of cytochrome c exhibits a very low conformational energy (-504 kcal/mol) and also closely resembles the X-ray structure (RMS deviation = 0.77 A for all atoms). However, a special treatment was required in order to alter the location of the phenyl ring of phenylalanine-82. In contrast to the originally published X-ray structure, which shows the phenyl ring pointing away from the heme, the phenyl ring in the computed structure is tucked into the heme crevice, in a position similar to that observed in the reduced form of tuna cytochrome c, in the oxidized form of Rhodospirillum rubrum cytochrome c2, and also in the recently determined structure of oxidized tuna cytochrome c.

The influence of amino acid substitutions on the conformational energy of cytochrome c

Conformational energies have been evaluated for each of the staggered side-chain conformations associated with the 261 amino acid substitutions known to occur among 60 eucaryotic species. At least 86% of these substitutions can be sterically accommodated (one at a time) within the structure of horse-heart cytochrome c resulting from conformational energy refinement. Simultaneous incorporation of all pertinent amino acid substitutions found in eight representative species into the refined horse-heart structure is also shown to be sterically possible, with few exceptions. In two cases (Pekin duck cytochrome with 10 substitutions and Samia cynthia cytochrome with 24 substitutions), all substitutions could be readily incorporated, and the total energies associated with their computed structures differed by less than 10 kcal/mol from that of horse-heart cytochrome c. In the cytochromes from rattlesnake (22 substitutions), tuna (18 substitutions), and Neurospora crassa (36 substitutions), tyrosine could not be substituted for phenylalanine at position 46, within the constraints of the calculations. However, when all of the remaining substitutions were incorporated into these three cytochromes, their computed conformational energies differed by less than 30 kcal/mol from that of horse-heart cytochrome c. Between two and four amino acid substitutions cause high energies in the cytochromes from human, baker's yeast, and cotton seed, but all of the remaining substitutions are consistent with a low energy conformation. These results suggest that the structures of homologous proteins may be even more similar than has previously been recognized. Substitutions of all possible amino acid types at the invariant positions (where all eucaryotic cytochromes c bear the same amino acid) have revealed some cases where different amino acids can be accommodated, thus demonstrating that the biological constraints on amino acid substitutions are often different from the purely steric constraints investigated in this work.

The amino acid sequence of cytochrome f from the brown alga Alaria esculenta (L.) Grev

Cytochrome f was isolated from the brown alga Alaria esculenta and the amino acid sequence was determined. The native haemoprotein has a molecular weight of 9800 and consists of a single polypeptide chain of 86 amino acid residues with a haem group bonded to cysteine residues at positions 14 and 17. The N-terminus is not acetylated and no methylated lysines were found. Sequences of three other algal cytochromes f were compared with that of Alaria and 22 out of 92 positions were common to the four sequences. One-half of these conserved sites occur between positions 49 and 63. Detailed evidence for the amino acid sequence of Alaria cytochrome has been deposited as Supplementary Publication SUP 50048 (6 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1975) 145, 5.

Change of cytochrome c structure during development of the mouse

The structure of cytochrome c during mouse development is investigated. For this purpose the amino acid sequence of cytochrome c of the adult mouse had to be determined. The structure of cytochrome c of adult differentiated mouse cells differs in two amino acid residues from the known amino acid sequence of rabbit cytochrome c. No indication of different forms of cytochrome c in the adult differentiated cells was obtained. The structure of cytochrome c from 11.5-day-old mouse embryos is identical with that of adult mouse tissues. Since germ cells after meiotic division are the immediate precursors of a new individual, the structure of cytochrome c from sperm-containing mice testes was investigated. By means of chromatography of the cytochrome c and of peptide maps and amino acid analyses of its tryptic peptides, it is shown that mouse testis contains two isocytochromes c in about equal amount. The structure of one of these two isocytochromes c is identical with the structure of the adult-type cytochrome c of mouse. The testis-specific cytochrome c, which is assumed to be located in the sperm cells, differs in 13 of its 104 amino acid residues from the adult-type cytochrome c. From comparison of the primary and the spatial structures of the adult-type and the sperm-type isocytochromes c with the known structures of cytochrome c of more than 65 different species it is concluded that the duplication of the cytochrome c structural gene, causing the existence of the two ontogenetic-specific isocytochromes c in mouse, has occurred early in the evolution of eucaryotes.

Crystalline adenylate kinase from carp muscle

1. The concentration of adenylate kinase in carp muscle is about 0.3 mg/g. An improved isolation procedure makes use of a dilute solution of the substrates, ATP and AMP, to elute the enzyme from a phosphocellulose column in overall yields of 60% before crystallization. By the hexokinase--pH-stat assay the specific activity is 3550 units/mg. The preparation has been found to be essentially homogeneous by dodecylsulfate gel electrophoresis, isoelectrofocusing and gel filtration. 2. The molecular weight has been determined to be 22000 by several methods. The absorbance of a 1% solution at 280 nm is 6.9 and the isoelectric point by electrofocusing is pH 5.9. 3. The crystals of carp adenylate kinase have the space group P4-1-22 or P4-3-22. 4. The amino acid composition has been determined. There is no tryptophan, no cystine. There is one amino acid residue each of cysteine and histidine which are at or close to the catalytic center. 5. Several peptides derived by tryptic hydrolysis have been isolated and identified with corresponding peptides of porcine adenylate kinase. Consideration is given to histidine and cysteine being a part of the active site.

Homology between bakers' yeast cytochrome b2 and liver microsomal cytochrome b5

The amino-acid sequence of the hemebinding region of bakers' yeast cytochrome b(2) [L-(+)-lactate dehydrogenase, EC 1.1.2.3] has been determined. It shows a strong similarity with the sequence of microsomal cytochrome b(5), and appears to be compatible with the same kind of peptide-chain folding, in agreement with data obtained previously by various physiochemical methods. The comparison shows that the fifth and sixth heme ligands must be histidine residues, thus substantiating previous conclusions drawn in particular from photooxidation experiments and nuclear magnetic resonance studies. The data reported in this paper suggest a common origin for the two proteins. Implications for their biochemical evolution are presented.

The purification and amino acid sequence of cytochrome C-552 from Euglena gracilis

Cytochrome c-552 from Euglena gracilis was purified and the amino acid sequence determined. The protein is a single peptide chain of 87 residues with the haem prosthetic group bound through two thioether linkages to two cysteine residues near the amino-terminal region. The amino acid sequence shows some similarities to mitochondrial cytochrome c and to two prokaryote c-type cytochromes. The sequence, taken with the known characteristics of cytochrome c-552, indicates that it is an f-type cytochrome. The possible functional and evolutionary significance of these features in common is discussed. Detailed evidence for the amino acid sequence of Euglena cytochrome f has been deposited as Supplementary Publication SUP 50027 at the British Library, Lending Division (formerly the National Lending Library for Science and Technology), Boston Spa, Yorks. LS23 7QB, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973) 131, 5.