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I. Transcription

  • Science, Vol. 292, Issue 5523, 1876-1882, June 8, 2001

    STRUCTURAL BIOLOGY:
    A Marvellous Machine for Making Messages

    Aaron Klug*

    The multisubunit enzyme RNA polymerase II (also called RNA polymerase b, Rpb, or Pol II) is the central enzyme of gene expression in eukaryotes. It reads the sequence of one strand of the DNA double helix (the template) and in so doing synthesizes messenger RNA (mRNA), which is then translated into protein. Two papers by Roger Kornberg's group (1, 2) on pages 1863 and 1876 of this issue go a long way toward helping us to understand the structural basis of transcription at the atomic level.

II. Proteins Unfolding Pathways

  • Science. 2000 Apr 7;288(5463):63-4.

STRUCTURAL BIOLOGY:
Unraveling a Membrane Protein

Jeffrey G. Forbes and George H. Lorimer

Atomic force microscopy (AFM) is an elegant technique in which a roving microscopic needle tip provides images of the surfaces of objects beneath it. In a Perspective, Forbes and Lorimer discuss how AFM can be applied to the step-wise unfolding of membrane proteins such as bacteriorhodopsin (Oesterhelt et al.). When the AFM tip becomes attached to points on the protein exposed on the membrane surface, the protein unfolds, helix by helix, as the tip is withdrawn.


The authors are in the Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742-2021, USA. E-mail: jf95@umail.umd.edu, gl48@umail.umd.edu 

Science 288,  7 Apr 2000, pp. 63 - 64

Click here to read
Protein folding and unfolding on a complex energy landscape.

Leeson DT, Gai F, Rodriguez HM, Gregoret LM, Dyer RB

Center for Nonlinear Studies, MS B258, and Bioscience Division, MS J586, Los Alamos National Laboratory, Los Alamos, NM 87545; and Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA 95064.

[Record supplied by publisher]

Recent theories of protein folding suggest that individual proteins within a large ensemble may follow different routes in conformation space from the unfolded state toward the native state and vice versa. Herein, we introduce a new type of kinetics experiment that shows how different unfolding pathways can be selected by varying the initial reaction conditions. The relaxation kinetics of the major cold shock protein of Escherichia coli (CspA) in response to a laser-induced temperature jump are exponential for small temperature jumps, indicative of folding through a two-state mechanism. However, for larger jumps, the kinetics become strongly nonexponential, implying the existence of multiple unfolding pathways. We provide evidence that both unfolding across an energy barrier and diffusive downhill unfolding can occur simultaneously in the same ensemble and provide the experimental requirements for these to be observed.

III. Protein-protein interaction

  • Nature 403, 623 (2000).

BIOCHEMISTRY: Assembling a Protein Jigsaw Puzzle

Scientists have reasoned that, like pieces of a jigsaw puzzle, if two proteins fit together, then this interaction is likely to contribute to in vivo function. Uetz et al. compare microarray and library variations of the yeast two-hybrid system as a step toward identifying the complete set of interactions that occur among the ~6000 yeast proteins. In the first approach, 6000 yeast colonies, each containing the activation domain of Gal4 fused to a different open reading frame (ORF), were mated to a separate set of hybrids containing the Gal4 DNA-binding domain fused to one of 192 ORFs. In the second approach, the 6000 ORF-containing varieties were pooled into a library, mated against DNA-binding domain--containing counterparts, and then analyzed in a semi-automated screen.

The microarray approach, although requiring significantly more work and time, provided more positive results per protein than the library approach. Furthermore, the pooling that occurs in the library approach may select against cells that are growing more slowly or mate less efficiently. A total of 957 possible interactions were identified by these approaches, many of which may help to classify proteins of known function but of unknown pathway. -- BJ

Albertha J. M. Walhout, Raffaella Sordella, Xiaowei Lu, James L. Hartley, Gary F. Temple, Michael A. Brasch, Nicolas Thierry-Mieg, and Marc Vidal. Protein Interaction Mapping in C. elegans Using Proteins Involved in Vulval. Science 287: 116-122. 

Stuart K. Kim. Reading the Worm Genome. Science 287: 52-53.

Can researchers find recipe for proteins and chips? Nature Volume 402 Number 6763 Page 718 - 719 (ng/01/news).

How to spot a protein in a crowd. Nature Volume 402 Number 6763 Page 716 - 717 (ng/01/news) Full Text

OPINIONS [Nature 402, 703 (1999)]: The promise of proteomics Analysing the entire set of proteins of an organism is a far bigger challenge than anything in genomics. The technological obstacles and biological complexities require, for now, a steady approach to that necessary goal. The inside of a cell is a crowded and dynamic place, where proteins are perpetually being created and discarded. Understanding the structures, interactions and functions of all of a cell's or organism's proteins is one of the grand goals of the post-genomic era, and has been given a disciplinary title of its own: proteomics. There are even some who want to develop a human proteome project. Is that premature, or even meaningful?

ANTON J. ENRIGHT, IOANNIS ILIOPOULOS, NIKOS C. KYRPIDES & CHRISTOS A. OUZOUNIS.   Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86 - 90 (1999) A large-scale effort to measure, detect and analyse protein–protein interactions using experimental methods is under way. These include biochemistry such as co-immunoprecipitation or crosslinking, molecular biology such as the two-hybrid system or phage display, and genetics such as unlinked noncomplementing mutant detection. Using the two-hybrid system, an international effort to analyse the complete yeast genome is in progress. Evidently, all these approaches are tedious, labour intensive and inaccurate. From a computational perspective, the question is how can we predict that two proteins interact from structure or sequence alone. Here we present a method that identifies gene-fusion events in complete genomes, solely based on sequence comparison. Because there must be selective pressure for certain genes to be fused over the course of evolution, we are able to predict functional associations of proteins. We show that 215 genes or proteins in the complete genomes of Escherichia coli, Haemophilus influenzae and Methanococcus jannaschii are involved in 64 unique fusion events. The approach is general, and can be applied even to genes of unknown function.

EDWARD M. MARCOTTE, MATTEO PELLEGRINI, MICHAEL J. THOMPSON, TODD O. YEATES & DAVID EISENBERG. A combined algorithm for genome-wide prediction of protein function. Nature 402, 83 - 86 (1999) The availability of over 20 fully sequenced genomes has driven the development of new methods to find protein function and interactions. Here we group proteins by correlated evolution, correlated messenger RNA expression patterns and patterns of domain fusion to determine functional relationships among the 6,217 proteins of the yeast Saccharomyces cerevisiae. Using these methods, we discover over 93,000 pairwise links between functionally related yeast proteins. Links between characterized and uncharacterized proteins allow a general function to be assigned to more than half of the 2,557 previously uncharacterized yeast proteins. Examples of functional links are given for a protein family of previously unknown function, a protein whose human homologues are implicated in colon cancer and the yeast prion Sup35.

ANDREJ ScaronALI Genomics: Functional links between proteins. Nature 402, 23 - 26 (1999) Andrej Scaronali is at the Laboratories of Molecular Biophysics, Pels Family Center for Biochemistry and Structural Biology, The Rockefeller University, 1230 York Avenue, New York, New York 10021, USA.
e-mail: sali@rockefeller.edu
 

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