List of biophysically important macromolecular crystal structures

From Wikipedia, the free encyclopedia
Jump to: navigation, search
Nucleosome X-ray crystal structure

Crystal structures of protein and nucleic acid molecules and their complexes are central to the practice of most parts of biophysics, and have shaped much of what we understand scientifically at the atomic-detail level of biology. Their importance is underlined by the United Nations declaring 2014 as the International Year of Crystallography, as the 100th anniversary of Max von Laue's 1914 Nobel prize for discovering the diffraction of X-rays by crystals. This chronological list of biophysically notable protein and nucleic acid structures is loosely based on a review in the Biophysical Journal.[1] The list includes all the first dozen distinct structures, those that broke new ground in subject or method, and those that became model systems for work in future biophysical areas of research.

Myoglobin[edit]

Myoglobin sketch
Alpha helix

1960 - Myoglobin was the very first high-resolution crystal structure of a protein molecule.[2] Myoglobin cradles an iron-containing heme group that reversibly binds oxygen for use in powering muscle fibers, and those first crystals were of myoglobin from the sperm whale, whose muscles need copious oxygen storage for deep dives. The myoglobin 3-dimensional structure is made up of 8 alpha-helices, and the crystal structure showed that their conformation was right-handed and very closely matched the geometry proposed by Linus Pauling, with 3.6 residues per turn and backbone hydrogen bonds from the peptide NH of one residue to the peptide CO of residue i+4. Myoglobin is a model system for many types of biophysical studies,[3] especially involving the binding process of small ligands such as oxygen and carbon monoxide.

Hemoglobin[edit]

Hemoglobin beta chain
Hemoglobin oxy/deoxy transition

1960 - The Hemoglobin crystal structure[4] showed a tetramer of two related chain types and was solved at much lower resolution than the monomeric myoglobin, but it clearly had the same basic 8-helix architecture (now called the "globin fold"). Further hemoglobin crystal structures at higher resolution [PDB 1MHB, 1DHB) soon showed the coupled change of both local and quaternary conformation between the oxy and deoxy states of hemoglobin,[5] which explains the cooperativity of oxygen binding in the blood and the allosteric effect of factors such as pH and DPG. For decades hemoglobin was the primary teaching example for the concept of allostery, as well as being an intensive focus of research and discussion on allostery. In 1909, hemoglobin crystals from >100 species were used to relate taxonomy to molecular properties.[6] That book was cited by Perutz in the 1938 report[7] of horse hemoglobin crystals that began his long saga to solve the crystal structure. Hemoglobin crystals are pleochroic - dark red in two directions and pale red in the third[6] - because of the orientation of the hemes, and the bright Soret band of the heme porphyrin groups is used in spectroscopic analysis of hemoglobin ligand binding.

HEW lysozyme ribbon

Hen-egg-white lysozyme[edit]

1965 - Hen-egg-white lysozyme (PDB file 1lyz).[8] was the first crystal structure of an enzyme (it cleaves small carbohydrates into simple sugars), used for early studies of enzyme mechanism.[9] It contained beta sheet (antiparallel) as well as helices, and was also the first macromolecular structure to have its atomic coordinates refined (in real space).[10] The starting material for preparation can be bought at the grocery store, and hen-egg lysozyme crystallizes very readily in many different space groups; it is the favorite test case for new crystallographic experiments and instruments. Recent examples are nanocrystals of lysozyme for free-electron laser data collection[11] and microcrystals for micro electron diffraction.[12]

Ribonuclease A ribbon drawing

Ribonuclease[edit]

1967 - Ribonuclease A (PDB file 2RSA)[13] is an RNA-cleaving enzyme stabilized by 4 disulfide bonds. It was used in Anfinsen's seminal research on protein folding which led to the concept that a protein's 3-dimensional structure was determined by its amino-acid sequence. Ribonuclease S, the cleaved, two-component form studied by Fred Richards, was also enzymatically active, had a nearly identical crystal structure (PDB file 1RNS),[14] and was shown to be catalytically active even in the crystal,[15] helping dispel doubts about the relevance of protein crystal structures to biological function.

Two domains of elastase

Serine proteases[edit]

1967 - The serine proteases are a historically very important group of enzyme structures, because collectively they illuminated catalytic mechanism (in their case, by the Ser-His-Asp "catalytic triad"), the basis of differing substrate specificities, and the activation mechanism by which a controlled enzymatic cleavage buries the new chain end to properly rearrange the active site.[16] The early crystal structures included chymotrypsin (PDB file 2CHA),[17] chymotrypsinogen (PDB file 1CHG),[18] trypsin (PDB file 1PTN),[19] and elastase (PDB file 1EST).[20] They also were the first protein structures that showed two near-identical domains, presumably related by gene duplication. One reason for their wide use as textbook and classroom examples was the insertion-code numbering system (hated by all computer programmers), which made Ser195 and His57 consistent and memorable despite the protein-specific sequence differences.

Papain[edit]

1968 - Papain

Carboxypeptidase, with Zn
CPA inhibitor

Carboxypeptidase[edit]

1969 - Carboxypeptidase A is a zinc metalloprotease. Its crystal structure (PDB file 1CPA)[21] showed the first parallel beta structure: a large, twisted, central sheet of 8 strands with the active-site Zn located at the C-terminal end of the middle strands and the sheet flanked on both sides with alpha helices. It is an exopeptidase that cleaves peptides or proteins from the carboxy-terminal end rather than internal to the sequence. Later a small protein inhibitor of carboxypeptidase was solved (PDB file 4CPA)[22] that mechanically stops the catalysis by presenting its C-terminal end just sticking out from between a ring of disulfide bonds with tight structure behind it, preventing the enzyme from sucking in the chain past the first residue.

Subtilisin[edit]

1969 - Subtilisin

Lactate dehydrogenase[edit]

1970 - Lactate dehydrogenase

Trypsin inhibitor[edit]

1970 - Basic pancreatic trypsin inhibitor, or BPTI,

Rubredoxin[edit]

1970 - Rubredoxin

SS-linked insulin monomer
Space-grown insulin crystals

Insulin[edit]

1971 - Insulin (PDB file 1INS)[23] is a hormone central to the metabolism of sugar and fat storage, and important in human diseases such as obesity and diabetes. It is biophysically notable for its Zn binding, its equilibrium between monomer, dimer, and hexamer states, its ability to form crystals in vivo, and its synthesis as a longer "pro" form which is then cleaved to fold up as the active 2-chain, SS-linked monomer. Insulin was a success of NASA's crystal-growth program on the space shuttle, producing bulk preparations of very uniform tiny crystals for controlled dosage.

Staphylococcal nuclease[edit]

1971 - Staphylococcal nuclease

Cytochrome C[edit]

1971 - Cytochrome C

T4 phage lysozyme[edit]

1974 - T4 phage lysozyme

Immunoglobulins[edit]

1974 - Immunoglobulins

Superoxide dismutase[edit]

1975 - Cu,Zn Superoxide dismutase

Transfer RNA[edit]

1976 - Transfer RNA

TIM ribbon drawing, PDB 1tim

Triose phosphate isomerase[edit]

1976 - Triose phosphate isomerase

Pepsin-like aspartic proteases[edit]

1976 - Rhizopuspepsin

1976 - Endothiapepsin

1976 - Penicillopepsin

Icosahedral viruses[edit]

1978 - Icosahedral virus

1981 - Dickerson B-form DNA dodecamer

1981 - Crambin

1985 - Calmodulin

1985 - DNA polymerase

1985 - Photosynthetic reaction center

CAP protein dimer on DNA, PDB 1cgp

Repressor/DNA interactions[edit]

1986 - Repressor/DNA interactions

1987 Major histocompatibility complex'

1987 Ubiquitin

1987 ROP protein

HIV-1 aspartic protease[edit]

1989 HIV-1 protease

1990 Bacteriorhodopsin

1991 GCN4 coiled coil

HIV-1 reverse transcriptase[edit]

1991 HIV-1 reverse transcriptase

1993 Beta helix of Pectate lyase

1994 Collagen

1994 Barnase/barstar complex

1994 F1 ATPase

1995 Heterotrimeric G proteins

1996 Green fluorescent protein

1996 CDK/cyclin complex

Kinesin dimer, PDB 3kin

Kinesin[edit]

1996 - Kinesin motor protein

1997 GroEL/ES chaperone

1997 Nucleosome

1998 Group I self-splicing intron

Topoisomerase Type I enzyme (blue) on double-helical DNA (by David Goodsell)

DNA topoisomerase[edit]

1998 - DNA topoisomerases perform the biologically important and necessary job of untangling DNA strands or helices that get entwined with each other or twisted too tightly during normal cellular processes such as the transcription of genetic information.

1998 Tubulin alpha/beta dimer

1998 Potassium channel

1998 Holliday junction

2000 Ribosome

2000 AAA+ ATPase

2002 Ankyrin repeats

2003 TOP7 protein design

2004 Cyanobacterial Circadian clock proteins

2004 Riboswitch

2006 Human exosome

2007 G-protein-coupled receptor

Half of a vault particle

Vault particle[edit]

2009 The Vault particle is an intriguing new discovery of a large hollow particle common in cells, with several different suggestions for its possible biological function. The crystal structures (PDB files 2zuo, 2zv4, 2zv5[24] and 4hl8[25]) show that each half of the vault is made up of 39 copies of a long 12-domain protein that swirl together to form the enclosure. Disorder at the very top and bottom ends suggests openings for possible access to the interior of the vault.

Free-electron laser crystallography[edit]

2010 - Free-electron laser crystallography

References[edit]

  1. ^ Richardson JS, Richardson DC (2014). "Biophysical highlights from 54 years of macromolecular crystallography". Biophysical Journal. 106: 510–525. doi:10.1016/j.bpj.2014.01.001. PMC 3945011Freely accessible. PMID 24507592. 
  2. ^ Kendrew JC, Dickerson RE, Strandberg BE, Davies DR, Phillips DC, Shore VC (1960). "Structure of myoglobin: A three-dimensional Fourier synthesis at 2Å resolution". Nature. 185 (4711): 422–427. doi:10.1038/185422a0. PMID 18990802. 
  3. ^ Frauenfelder H, McMahon BH, Fenimore PW (2003). "Myoglobin: the hydrogen atom of biology and a paradigm of complexity". Proceedings of the National Academy of Sciences USA. 100: 8615–8617. doi:10.1073/pnas.1633688100. 
  4. ^ Perutz MF, Rossmann MG, Cullis AF, Muirhead H, North AC (1960). "Structure of haemoglobin: A three-dimensional Fourier synthesis at 5.5-Å resolution, obtained by X-ray analysis". Nature. 185 (4711): 416–422. doi:10.1038/185416a0. PMID 18990801. 
  5. ^ Perutz MF (1970). "Stereochemistry of Cooperative Effects in Haemoglobin: Haem–Haem Interaction and the Problem of Allostery". Nature. 228 (5273): 726–734. doi:10.1038/228726a0. 
  6. ^ a b Edward Tyson Reichert & Amos Peaslee Brown (1909). The Differentiation and Specificity of Corresponding Proteins and other Vital Substances in Relation to Biological Classification and Organic Evolution: The Crystallography of Hemoglobins. Washington, DC: Carnegie Institution. 
  7. ^ Bernal JD, Fankuchen I, Perutz M (1938). "X-ray syudy of chymotrypsin and hemoglobin". Nature. 141: 523–524. doi:10.1038/141523a0. 
  8. ^ Blake CC, Koenig DF, Mair GA, North AC, Phillips DC, Sarma VR (1965). "Structure of hen egg-white lysozyme: A three-dimensional Fourier synthesis at 2Å resolution". Nature. 206 (4986): 757–761. doi:10.1038/206757a0. PMID 5891407. 
  9. ^ Warshel A, Levitt M (1976). "Theoretical studies of enzymic reactions: Dielectric, electrostatic, and steric stabilization of the carbonium ion in the reaction of lysozyme". J Mol Biol. 103: 227–49. doi:10.1016/0022-2836(76)90311-9. PMID 985660. 
  10. ^ Diamond R (1974). "Real-space refinement of the structure of hen egg-white lysozyme". Journal of Molecular Biology. 82: 371–374. doi:10.1016/0022-2836(74)90598-1. 
  11. ^ Boutet S, Lomb L, Williams GJ, et al. (2012). "High-resolution protein structure determination by serial femtosecond crystallography". Science. 337: 362–364. doi:10.1126/science.1217737. 
  12. ^ Shi D, Nannenga BL, Iadenza MG, Gonen T (2013). "Three-dimensional electron crystallography of protein microcrystals". Elife. 2: e01345–e01345. doi:10.7554/elife.01345. 
  13. ^ Kartha G, Bello J, Harker D (1967). "Tertiary structure of ribonuclease". Nature. 213 (5079): 862–865. doi:10.1038/213862a0. PMID 6043657. 
  14. ^ Wyckoff HW, Hardman KD, Allewell NM, Inagami T, Johnson LN, Richards FM (1967). "The structure of ribonuclease-S at 3.5 Å resolution". Journal of Biological Chemistry. 242: 3984–3988. 
  15. ^ Doscher MS, Richards FM (1963). "The activity of an enzyme in the crystalline state: Ribonuclease-S". Journal of Biological Chemistry. 238: 2399–2406. 
  16. ^ Dickerson RE, Geis I (1969). Structure and Action of Proteins. New York: Harper. 
  17. ^ Matthews BW, Sigler PB, Henderson R, Blow DM (1967). "Three-dimensional structure of tosyl-α-chymotrypsin". Nature. 214 (5089): 652–656. doi:10.1038/214652a0. 
  18. ^ Freer ST, Kraut J, Robertus JD, Tonle H, Wright HT (1970). "Chymotrypsinogen: 2.5-Å crystal structure, comparison with α-chymotrypsin, and implications for zymogen activation". Biochemistry. 9 (9): 1997–2009. doi:10.1021/bi00811a022. PMID 5442169. 
  19. ^ Fehlhammer H, Bode W (1975). "The refined crystal structure of bovine beta-trypsin at 1.8Å resolution, II. Crystallographic refinement, calcium binding site and active site at pH 7.0". Journal of Molecular Biology. 98: 693–697. doi:10.1016/s0022-2836(75)80005-2. 
  20. ^ Sawyer L, Shotton DM, Campbell JW, Ladner RC (1978). "The atomic structure of crystalline porcine pancreatic elastase at 2.5Å resolution: comparison with the structure of alpha-chymotrypsin". Journal of Molecular Biology. 118: 137–208. doi:10.1016/0022-2836(78)90412-6. 
  21. ^ Lipscomb WN; Hartsuck JA; Reeke GN; Quiocho FA; Bethge PH; Ludwif=g ML; Steitz TA; Muirhead H; Coppola JC (1969). "The structure of carboxypeptidase A, VII. The 2.0-Å resolution studies of the enzyme and of its complex with glycyltyrosine, and mechanistic deductions". Brookhaven Symposia in Biology. 21: 24–90. 
  22. ^ Rees DC, Lipscomb WN (1982). "Refined crystal structure of the potato inhibitor complex of carboxypeptidase A at 2.5 A resolution". Journal of Molecular Biology. 160: 475–498. doi:10.1016/0022-2836(82)90309-6. 
  23. ^ Blundell TL, Cutfield JF, Cutfield SM, Dodson EJ, Dodson GG, Hodgkin DC, Mercola DA, Vijayan M (1971). "Atomic positions in rhombohedral 2-zinc insulin crystals". Nature. 231 (5304): 506–511. doi:10.1038/231506a0. PMID 4932997. 
  24. ^ Tanaka H, Kato K, Yamashita E, Sumizawa T, Zhou Y, Yau M, Iwasaki K, Yoshimura M, Tsukihara T (2009). "The Structure of Rat Liver Vault at 3.5 Angstrom Resolution". Science. 323 (5912): 384–388. doi:10.1126/science.1164975. PMID 19150846. 
  25. ^ Casanas A, Querol-Audi J, Guerra P, Pous J, Tanaka H, Tsukihara T, Verdaguer N, Fita I (2013). "New features of vault architecture and dynamics revealed by novel refinement using the deformable elastic network approach". Acta Crystallographica. D69 (Pt 6): 1054–1061. doi:10.1107/S0907444913004472. PMID 23695250.