- Email: [email protected]
Of chemical promiscuity and its structural background
474
News & Comment
concerns about the proposal from the European Commission for the Framework Programme 2002–2006 for Research. Among the points highlighted by the statement, was that of spreading concern that proposals for large-scale integrated projects could disadvantage smaller research groups and enterprises active in innovative research. The three organizations also praised the added support to research mobility (a key problem) contained in the Framework Programme proposal. Tuned on the same issue, the European Commission has recently released a communication that sets out a strategy to overcome obstacles to research mobility in Europe which, in turn, will contribute, in the Commission’s opinion, to galvanize the creation of the European Research Area. AR (http://europa.eu.int/eur-lex/en/com/cnc/ 2001/com2001_0331en01.pdf; http://www.esf.org/update/news/01/ statement.html)
Get a random move on! Randomness might be the ultimate explanation of several chemomechanical energy conversions in molecular and cellular biology. Ronald Fox and Mee Hyang Choi from the Georgia Institute of Technology (Atlanta, Georgia, USA) have reanalysed measured data for the motion of the kinesin motor protein along microtubules with a new perspective [Phys. Rev. E (2001) 63, 051901]. Kinesins ‘travel’ along microtubules while undergoing an ATP-activated attachment–detachment cycle coordinated by binding sites on microtubules. The new study revealed that what first appeared to be a concerted motion might instead be a ‘rectified Brownian movement’, a form of random motion powered by thermal energy. The model implies that, in this case, the metabolic free-energy currency of ATP does no mechanical work directly, this instead being done by thermal energy. Fox and Choi argue that, in kinesin, ATP performs a switching role, changing the protein conformation and its binding affinity. The randomness of the thermal Brownian motion is thus harnessed and constrained by conditions created by the ATP switching, resulting in a netdirected kinesin motion along the microtubule. AR (http://gtresearchnews.gatech.edu/ newsrelease/KINESIN.html) http://tibs.trends.com
TRENDS in Biochemical Sciences Vol.26 No.8 August 2001
Of chemical promiscuity and its structural background
Cytochrome P450-3A is a key protein in the liver responsible for metabolizing >60% of drugs ingested by humans. Expression of this protein is activated by the human nuclear pregnane X receptor (hPXR) in response to a wide variety of xenobiotics. Being characterized by the peculiar ability to bind to a large variety of drugs and toxins, hPXR is known to play a crucial role in mediating dangerous drug–drug interactions. Chemists at the University of North Carolina (UNC; Chapel Hill) and GlaxoSmithKline have now determined high-resolution crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterollowering drug SR12813 [Science (2001) 292, 2329–2333]. A large hydrophobic ligandbinding pocket containing a small number of polar residues was identified in the hPXR structure, and the nature and position of these polar residues were found to be crucial for the precise pharmacologic activation profile of the receptor. ‘These results will further help us to identify and prevent dangerous drug–drug interactions in humans and to understand how drugs are metabolized and disposed of’, said Matthew Redinbo, Assistant Professor of Chemistry at UNC. AR
Speeding up enzyme evolution Enzyme evolution is thought to proceed largely by gene duplication and the propagation of slightly deleterious amino acid substitutions. Low stability and poor catalytic rates are properties shared by many newly evolved enzymes that arise as gene duplication events in which selection for stability and/or turnover is released while mutations accumulate that finally result in an alteration of function. Starting from this model, Edward Whittle and John Shanklin in the Biology Dept of Brookhaven National Laboratory (Upton, New York, USA), now show that it is possible to reenginner
archetypal enzymes to achieve altered substrate specificities characteristic of recently evolved enzymes while retaining the desired stability and/or turnover characteristics of the parental paralog [J. Biol. Chem. (2001) 276, 21500–21505)]. Working with soluble castor ∆9-18:0-acyl carrier protein (ACP) desaturase, an enzyme which introduces a double bond region specifically into a saturated acyl-ACP substrate, Whittle and Shanklin used combinatorial saturation mutagenesis at six amino acid positions known to affect substrate specificity to maximize the likelihood of identifying variants with desired improvements in turnover rates. Upon identification of two key substitutions, namely T117R and G188L, researchers engineered back these changes into otherwise wild-type desaturase. Remarkably, they obtained an enzyme with significant preference for 16-carbon substrates but with kinetic parameters similar to those of wild-type desaturase for 18-carbon substrate, showing that is possible to alter the specificity of a desaturase (and most probably of other enzymes) without substantial degradation of its kinetic parameters. The engineered enzyme had a specific activity for 16-carbon 100 times higher than known natural 16-carbon specific desaturases. AR (http://www.bnl.gov/bnlweb/pubaf/pr/ bnlpr061301.htm)
Networking proteome people On 11 June, the Proteome Society launched its new website, which is intended to operate as a virtual forum for information exchange for those interested in functional genomics and proteomics. Aspects covered will include bioinformatics, separation and sequencing techniques, and techniques involving the structure and function of proteins. The initiative aims to encourage global collaboration between scientists from a variety of disciplines centering around proteomic research. ‘An online interface is essential for fostering collaboration in this international community’, said Cara Wykowski, the Society’s executive director. Founded in San Francisco in June 1997 as the Proteome Club, the Proteome Society has ~400 members in 12 countries. AR (http://www.proteome.org)
0968-0004/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.
Andrea Rinaldi [email protected]
News & Comment
concerns about the proposal from the European Commission for the Framework Programme 2002–2006 for Research. Among the points highlighted by the statement, was that of spreading concern that proposals for large-scale integrated projects could disadvantage smaller research groups and enterprises active in innovative research. The three organizations also praised the added support to research mobility (a key problem) contained in the Framework Programme proposal. Tuned on the same issue, the European Commission has recently released a communication that sets out a strategy to overcome obstacles to research mobility in Europe which, in turn, will contribute, in the Commission’s opinion, to galvanize the creation of the European Research Area. AR (http://europa.eu.int/eur-lex/en/com/cnc/ 2001/com2001_0331en01.pdf; http://www.esf.org/update/news/01/ statement.html)
Get a random move on! Randomness might be the ultimate explanation of several chemomechanical energy conversions in molecular and cellular biology. Ronald Fox and Mee Hyang Choi from the Georgia Institute of Technology (Atlanta, Georgia, USA) have reanalysed measured data for the motion of the kinesin motor protein along microtubules with a new perspective [Phys. Rev. E (2001) 63, 051901]. Kinesins ‘travel’ along microtubules while undergoing an ATP-activated attachment–detachment cycle coordinated by binding sites on microtubules. The new study revealed that what first appeared to be a concerted motion might instead be a ‘rectified Brownian movement’, a form of random motion powered by thermal energy. The model implies that, in this case, the metabolic free-energy currency of ATP does no mechanical work directly, this instead being done by thermal energy. Fox and Choi argue that, in kinesin, ATP performs a switching role, changing the protein conformation and its binding affinity. The randomness of the thermal Brownian motion is thus harnessed and constrained by conditions created by the ATP switching, resulting in a netdirected kinesin motion along the microtubule. AR (http://gtresearchnews.gatech.edu/ newsrelease/KINESIN.html) http://tibs.trends.com
TRENDS in Biochemical Sciences Vol.26 No.8 August 2001
Of chemical promiscuity and its structural background
Cytochrome P450-3A is a key protein in the liver responsible for metabolizing >60% of drugs ingested by humans. Expression of this protein is activated by the human nuclear pregnane X receptor (hPXR) in response to a wide variety of xenobiotics. Being characterized by the peculiar ability to bind to a large variety of drugs and toxins, hPXR is known to play a crucial role in mediating dangerous drug–drug interactions. Chemists at the University of North Carolina (UNC; Chapel Hill) and GlaxoSmithKline have now determined high-resolution crystal structures of the ligand-binding domain of hPXR both alone and in complex with the cholesterollowering drug SR12813 [Science (2001) 292, 2329–2333]. A large hydrophobic ligandbinding pocket containing a small number of polar residues was identified in the hPXR structure, and the nature and position of these polar residues were found to be crucial for the precise pharmacologic activation profile of the receptor. ‘These results will further help us to identify and prevent dangerous drug–drug interactions in humans and to understand how drugs are metabolized and disposed of’, said Matthew Redinbo, Assistant Professor of Chemistry at UNC. AR
Speeding up enzyme evolution Enzyme evolution is thought to proceed largely by gene duplication and the propagation of slightly deleterious amino acid substitutions. Low stability and poor catalytic rates are properties shared by many newly evolved enzymes that arise as gene duplication events in which selection for stability and/or turnover is released while mutations accumulate that finally result in an alteration of function. Starting from this model, Edward Whittle and John Shanklin in the Biology Dept of Brookhaven National Laboratory (Upton, New York, USA), now show that it is possible to reenginner
archetypal enzymes to achieve altered substrate specificities characteristic of recently evolved enzymes while retaining the desired stability and/or turnover characteristics of the parental paralog [J. Biol. Chem. (2001) 276, 21500–21505)]. Working with soluble castor ∆9-18:0-acyl carrier protein (ACP) desaturase, an enzyme which introduces a double bond region specifically into a saturated acyl-ACP substrate, Whittle and Shanklin used combinatorial saturation mutagenesis at six amino acid positions known to affect substrate specificity to maximize the likelihood of identifying variants with desired improvements in turnover rates. Upon identification of two key substitutions, namely T117R and G188L, researchers engineered back these changes into otherwise wild-type desaturase. Remarkably, they obtained an enzyme with significant preference for 16-carbon substrates but with kinetic parameters similar to those of wild-type desaturase for 18-carbon substrate, showing that is possible to alter the specificity of a desaturase (and most probably of other enzymes) without substantial degradation of its kinetic parameters. The engineered enzyme had a specific activity for 16-carbon 100 times higher than known natural 16-carbon specific desaturases. AR (http://www.bnl.gov/bnlweb/pubaf/pr/ bnlpr061301.htm)
Networking proteome people On 11 June, the Proteome Society launched its new website, which is intended to operate as a virtual forum for information exchange for those interested in functional genomics and proteomics. Aspects covered will include bioinformatics, separation and sequencing techniques, and techniques involving the structure and function of proteins. The initiative aims to encourage global collaboration between scientists from a variety of disciplines centering around proteomic research. ‘An online interface is essential for fostering collaboration in this international community’, said Cara Wykowski, the Society’s executive director. Founded in San Francisco in June 1997 as the Proteome Club, the Proteome Society has ~400 members in 12 countries. AR (http://www.proteome.org)
0968-0004/01/$ – see front matter © 2001 Elsevier Science Ltd. All rights reserved.
Andrea Rinaldi [email protected]