WHY MACROMOLECULAR STRUCTURE?
Why Do Scientists Study Structure? Biological function operates through structure. The genetic code is expressed through structure. 20 th century physicists developed the tools that enable us to see structures and thus to understand function.
60 YEARS OF MACROMOLECULAR STRUCTURE DETERMINATION
The Start of Protein Structure 1934 Dorothy Crowfoot (later Hodgkin*) and JD Bernal photograph X-ray diffraction from protein crystals 1951* Linus Pauling and Robert Corey build models of α-helix and β- sheets from X-ray data Linus Pauling and Robert Corey For the history of this discovery, see Eisenberg www.pnas.org/cgi/doi/10.1073/pnas.2034522100
Isadore Fankuchen, Dorothy Crowfoot, JD Bernal, Mrs. Fankuchen
The Big Developments of the 1950s Max Perutz discovers that multiple isomorphous replacement can yield the phases of diffracted X-rays, giving the structures of proteins Perutz graduate student Francis Crick and postdoc James Watson use X-ray data from Rosalind Franklin to build a model of DNA: April 1953
James Watson and Francis Crick
Structural Biology Fulfills Its Promise 1953* Watson, Crick, Rosalind Franklin & Wilkins use X-ray fiber diffraction to determine DNA structure 1960* Kendrew & Perutz determine structures for myoglobin & hemoglobin
1962 Nobel Prizes Wilkins Perutz Crick John Steinbeck Watson Kendrew
Rosalind Franklin (1920-1958) The book strikes something of a middle ground: Franklin was instrumental in discovering the structure of DNA, but she wasn't altogether ignored. As Maddox tells Howard Berkes for All Things Considered, it was Franklin's photograph of the DNA molecule that sparked a scientific revolution. Wilkins showed Watson the photo, and, Watson said, "My jaw fell open and my pulse began to race." The photo showed, for the first time, the essential structure of DNA -- the double-helix shape, which also indicated its method of replication. It was Franklin's photographic skills that made the discovery possible, says Maddox. "She could take photographs of crystals and interpret the patterns." She had "a particular genius at aligning hand and mind. She did not know the other men were using her research upon which to base the article that appeared in the journal Nature. She didn't complain either. This may be thanks to her upbringing, says Maddox. Franklin "didn't do anything that would invite criticism (this was) bred into her. Brenda Maddox, Rosalind Franklin: the Dark Lady of DNA, 2002, HarperCollins She wouldn't share in the Nobel Prize either. Maddox says this not because Franklin was overlooked, but because she was dead. The award is not given out posthumously. Franklin was diagnosed with ovarian cancer in 1956 at age 37, and died two years later, without an award, but not without recognition -- eventually. [Oct. 6, 2002 NPR (National Public Radio)]
More Firsts for Structural Biology 1978 Steve Harrison determines first plant virus structure: tomato bushy stunt virus 1985 Michael Rossmann and Jim Hogle determine first animal virus structures: polio, rhino 1982* Aaron Klug determines trna and tobacco mosaic virus structures 1985* Michel & Huber determine first membrane protein structure 1997* Walker, Boyer et al. ATPase structure 2000* Yonath, Steitz, Noller, Ribosome structure 2002* Wuthrich: NMR of macromolecules based on: 1946* Purcell & Bloch: NMR, 1992* Earnst: 2D NMR 2003* Rod MacKinnon determines K + channel structure 2006* Roger Kornberg determines RNA polymerase II
Ramakrishnan/Steitz/Yonath Chemistry 2009 X
Chapter 1 THE BUILDING BLOCKS
Hierarchy of Protein Structure Description
Proteins Are Polypeptide Chains Protein = (peptide unit) Successful polypeptide bonds: main chain or backbone
The Genetic Code Specifies 20 Different Amino Acid Side Chains Nonpolar and hydrophobic Polar and hydrophilic ("water loving") Acidic ("carboxy" group) Basic ("amine" group)
The Genetic Code Specifies 20 Different Amino Acid Side Chains
All Amino Acids in Protein Have the L-form Levorotary Dextrorotary
Cysteines Can Form Disulfide Bridges
Peptide Units Are Building Blocks of Protein Structures
Peptide Units Are Building Blocks of Protein Structures The only degrees of freedom: N-Cα bond: phi (φ) > C -N-Cα -C Cα -C bond: psi (ψ) -> N-Cα-C -N Dihedral (torsion) angles: angles between two planes
Ramachandran Plot A Ramachandran plot or (φ, ψ) plot: a way to visualize φ (x-axis) and ψ (y-axis) of amino acid residues in protein structure [Ramachandran GN, Ramakrishnan C, Sasisekharan V (1963). Stereochemistry of polypeptide chain configurations. J. Mol. Biol. 7(1):95-99]
Glycine Residues Can Adopt Many Different Conformations ψ φ Glycine
Certain Side-Chain Conformations Are Energetically Favorable: Rotamers
Many Proteins Contain Intrinsic Metal Atoms - Excellent ligands: His, Cys, Asp, Glu, H 2 O - Common metals: iron, zinc, magnesium, calcium Redox center of ribonucleotide reductase Alcohol dehydrogenase