Structural divergence and distant relationships in proteins: evolution of the globins.

The globin family has long been known from studies of approximately 150-residue proteins such as vertebrate myoglobins and haemoglobins. Recently, this family has been enriched by the investigation of the sequences and structures of truncated globins, which have the same basic topology but are approximately 30 residues shorter and exhibit functions other than the familiar one of binding diatomic ligands. The divergence of protein sequences, structures and functions reveals Nature's exploration of the potential inherent in a folding pattern, that is, the topology of the native structure. The observation of what remains constant and what varies during the evolution of a protein family reveals essential features of structure and function. Study of proteins with a wide range of divergence can therefore sharpen our understanding of how different amino acid sequences can determine similar three-dimensional structures. Globins have provided, and continue to provide, interesting material for such studies.

[1]  M. Bolognesi,et al.  Nonvertebrate hemoglobins: structural bases for reactivity. , 1997, Progress in biophysics and molecular biology.

[2]  M. Nardini,et al.  The 109 residue nerve tissue minihemoglobin from Cerebratulus lacteus highlights striking structural plasticity of the alpha-helical globin fold. , 2002, Structure.

[3]  A. Pesce,et al.  Crystal structure of cytoglobin: the fourth globin type discovered in man displays heme hexa-coordination. , 2004, Journal of molecular biology.

[4]  R. Hardison,et al.  A brief history of hemoglobins: plant, animal, protist, and bacteria. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Suman Kundu,et al.  Plants, humans and hemoglobins. , 2003, Trends in plant science.

[6]  Veronica Morea,et al.  The Truncated Oxygen-avid Hemoglobin from Bacillus subtilis , 2005, Journal of Biological Chemistry.

[7]  D. Rousseau,et al.  A cooperative oxygen-binding hemoglobin from Mycobacterium tuberculosis. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[8]  Martino Bolognesi,et al.  Truncated Hemoglobins: A New Family of Hemoglobins Widely Distributed in Bacteria, Unicellular Eukaryotes, and Plants* 210 , 2002, The Journal of Biological Chemistry.

[9]  M. Alam,et al.  Globin-coupled sensors, protoglobins, and the last universal common ancestor. , 2005, Journal of inorganic biochemistry.

[10]  M. Perutz,et al.  The crystal structure of human deoxyhaemoglobin at 1.74 A resolution. , 1984, Journal of molecular biology.

[11]  S. Phillips,et al.  Structure and refinement of oxymyoglobin at 1.6 A resolution. , 1980, Journal of molecular biology.

[12]  T. Burmester,et al.  Cytoglobin: a novel globin type ubiquitously expressed in vertebrate tissues. , 2002, Molecular biology and evolution.

[13]  P. Kallio,et al.  Bacterial hemoglobins and flavohemoglobins: versatile proteins and their impact on microbiology and biotechnology. , 2003, FEMS microbiology reviews.

[14]  Alessandra Pesce,et al.  Human brain neuroglobin structure reveals a distinct mode of controlling oxygen affinity. , 2003, Structure.

[15]  M. Blaxter,et al.  A Hemoglobin with an Optical Function* , 2000, The Journal of Biological Chemistry.

[16]  D. Kraus,et al.  Hemoglobins of the Lucina pectinata/bacteria symbiosis. I. Molecular properties, kinetics and equilibria of reactions with ligands. , 1990, The Journal of biological chemistry.

[17]  J. C. Kendrew,et al.  Structure and function of haemoglobin: II. Some relations between polypeptide chain configuration and amino acid sequence , 1965 .

[18]  D. Rousseau,et al.  Structural investigations of the hemoglobin of the cyanobacterium Synechocystis PCC6803 reveal a unique distal heme pocket. , 2000, European journal of biochemistry.

[19]  M. Alam,et al.  Ancestral hemoglobins in Archaea. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  R. Weber,et al.  Functional adaptation and its molecular basis in vertebrate hemoglobins, neuroglobins and cytoglobins , 2004, Respiratory Physiology & Neurobiology.

[21]  M. Hargrove,et al.  A Ubiquitously Expressed Human Hexacoordinate Hemoglobin* , 2002, The Journal of Biological Chemistry.

[22]  Alessandra Pesce,et al.  Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins. , 2005, Journal of inorganic biochemistry.

[23]  M. Bolognesi,et al.  Cyanide binding to truncated hemoglobins: a crystallographic and kinetic study. , 2004, Biochemistry.

[24]  S. Kundu,et al.  Crystallographic analysis of synechocystis cyanoglobin reveals the structural changes accompanying ligand binding in a hexacoordinate hemoglobin. , 2004, Journal of molecular biology.

[25]  R. Watts,et al.  Human Neuroglobin, a Hexacoordinate Hemoglobin That Reversibly Binds Oxygen* , 2001, Journal of Biological Chemistry.

[26]  Kenneth A. Johnson,et al.  The X-ray Structure of Ferric Escherichia coliFlavohemoglobin Reveals an Unexpected Geometry of the Distal Heme Pocket* , 2002, The Journal of Biological Chemistry.

[27]  M. Couture,et al.  Purification and spectroscopic characterization of a recombinant chloroplastic hemoglobin from the green unicellular alga Chlamydomonas eugametos. , 1996, European journal of biochemistry.

[28]  M. Perutz,et al.  Structure of hemoglobin. , 1960, Brookhaven symposia in biology.

[29]  G G Dodson,et al.  The structure of deoxy- and oxy-leghaemoglobin from lupin. , 1995, Journal of molecular biology.

[30]  M Bolognesi,et al.  A novel two‐over‐two α‐helical sandwich fold is characteristic of the truncated hemoglobin family , 2000, The EMBO journal.

[31]  R. Poole,et al.  Nitric oxide and nitrosative stress tolerance in bacteria. , 2005, Biochemical Society transactions.

[32]  A. Lesk,et al.  How different amino acid sequences determine similar protein structures: the structure and evolutionary dynamics of the globins. , 1980, Journal of molecular biology.

[33]  O. H. Kapp,et al.  Adventitious variability? The amino acid sequences of nonvertebrate globins. , 1993, Comparative biochemistry and physiology. B, Comparative biochemistry.

[34]  S. Vinogradov The structure of invertebrate extracellular hemoglobins (erythrocruorins and chlorocruorins). , 1985, Comparative biochemistry and physiology. B, Comparative biochemistry.

[35]  L. Pauling,et al.  Sickle cell anemia a molecular disease. , 1949, Science.

[36]  Jindong Zhao,et al.  Truncated hemoglobin from the cyanobacterium Synechococcus sp. PCC 7002: evidence for hexacoordination and covalent adduct formation in the ferric recombinant protein. , 2002, Biochemistry.

[37]  S N Vinogradov,et al.  Nonvertebrate hemoglobins: functions and molecular adaptations. , 2001, Physiological reviews.

[38]  Paolo Ascenzi,et al.  A TyrCD1/TrpG8 hydrogen bond network and a TyrB10—TyrCD1 covalent link shape the heme distal site of Mycobacterium tuberculosis hemoglobin O , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[39]  Crystal structure of oxygenated Scapharca dimeric hemoglobin at 1.7-A resolution. , 1994, The Journal of biological chemistry.

[40]  E. Myers,et al.  Basic local alignment search tool. , 1990, Journal of molecular biology.

[41]  H. Paerl,et al.  GlbN (cyanoglobin) is a peripheral membrane protein that is restricted to certain Nostoc spp , 1996, Journal of bacteriology.

[42]  Sudhir Kumar,et al.  MEGA2: molecular evolutionary genetics analysis software , 2001, Bioinform..

[43]  A M Lesk,et al.  Comparison of the structures of globins and phycocyanins: Evidence for evolutionary relationship , 1990, Proteins.

[44]  Max F. Perutz,et al.  Mechanisms of Cooperativity and Allosteric Regulation in Proteins , 1990 .

[45]  S. Schaeffer,et al.  Sulfide binding is mediated by zinc ions discovered in the crystal structure of a hydrothermal vent tubeworm hemoglobin. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[46]  S. Vinogradov,et al.  Mass spectrometric composition and molecular mass of Lumbricus terrestris hemoglobin: a refined model of its quaternary structure. , 1996, Journal of molecular biology.

[47]  Geoffrey J. Barton,et al.  The Jalview Java alignment editor , 2004, Bioinform..

[48]  Benno P. Schoenborn,et al.  Neutron diffraction reveals oxygen–histidine hydrogen bond in oxymyoglobin , 1981, Nature.

[49]  V. Ingram,et al.  A Specific Chemical Difference Between the Globins of Normal Human and Sickle-Cell Anæmia Hæmoglobin , 1956, Nature.

[50]  A. Lesk,et al.  Determinants of a protein fold. Unique features of the globin amino acid sequences. , 1987, Journal of molecular biology.

[51]  C Chothia,et al.  Haemoglobin: the structural changes related to ligand binding and its allosteric mechanism. , 1979, Journal of molecular biology.

[52]  B. Wittenberg,et al.  Truncated hemoglobin HbN protects Mycobacterium bovis from nitric oxide , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[53]  L. Tisa,et al.  Hemoglobin in five genetically diverse Frankia strains. , 2002, Canadian journal of microbiology.

[54]  T. Egawa,et al.  Structural and functional properties of hemoglobins from unicellular organisms as revealed by resonance Raman spectroscopy. , 2005, Journal of inorganic biochemistry.

[55]  T. Burmester,et al.  Globin genes are present in Ciona intestinalis. , 2003, Molecular biology and evolution.

[56]  M Brunori,et al.  Mini-myoglobin: preparation and reaction with oxygen and carbon monoxide. , 1986, Journal of molecular biology.

[57]  Thomas Hankeln,et al.  A vertebrate globin expressed in the brain , 2000, Nature.

[58]  Y P Chen,et al.  The Crystal Structure and Amino Acid Sequence of Dehaloperoxidase from Amphitrite ornata Indicate Common Ancestry with Globins* , 2000, The Journal of Biological Chemistry.

[59]  M. Potts,et al.  Myoglobin in a Cyanobacterium , 1992, Science.

[60]  Y Van de Peer,et al.  Globins in nonvertebrate species: dispersal by horizontal gene transfer and evolution of the structure-function relationships. , 1996, Molecular biology and evolution.

[61]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[62]  T. Takagi,et al.  Protozoan myoglobin from Paramecium caudatum. Its unusual amino acid sequence. , 1989, Journal of molecular biology.

[63]  J. Changeux,et al.  ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL. , 1965, Journal of molecular biology.

[64]  Joel Friedman,et al.  Heme-Ligand Tunneling in Group I Truncated Hemoglobins*[boxs] , 2004, Journal of Biological Chemistry.

[65]  R. Hardison THE EVOLUTION OF HEMOGLOBIN , 1999 .

[66]  M Bolognesi,et al.  Mycobacterium tuberculosis hemoglobin N displays a protein tunnel suited for O2 diffusion to the heme , 2001, The EMBO journal.

[67]  David Dantsker,et al.  Reactions of Mycobacterium tuberculosis truncated hemoglobin O with ligands reveal a novel ligand-inclusive hydrogen bond network. , 2003, Biochemistry.

[68]  Alessandra Pesce,et al.  The Redox State of the Cell Regulates the Ligand Binding Affinity of Human Neuroglobin and Cytoglobin* , 2003, Journal of Biological Chemistry.

[69]  R. Huber,et al.  The structure of oxy-erythrocruorin at 1.4 X resolution. , 1978, Journal of molecular biology.

[70]  Arthur M. Lesk,et al.  Introduction to protein architecture : the structural biologyof proteins , 2001 .

[71]  J. Kendrew,et al.  A Three-Dimensional Model of the Myoglobin Molecule Obtained by X-Ray Analysis , 1958, Nature.

[72]  J. Lecomte,et al.  Characterization of the heme–histidine cross-link in cyanobacterial hemoglobins from Synechocystis sp. PCC 6803 and Synechococcus sp. PCC 7002 , 2004, JBIC Journal of Biological Inorganic Chemistry.

[73]  Nicolas Carels,et al.  Genome Properties of the Diatom Phaeodactylum tricornutum 212 , 2002, Plant Physiology.