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The high-resolution structure of halophilic malate dehydrogenase (hMDH) from the archaebacterium Haloarcula marismortui was determined by x-ray crystallography. Comparison of the three-dimensional structures of hMDH and its nonhalophilic congeners reveals structural features that may promote the stability of hMDH at high salt concentrations. These features include an excess of acidic over basic residues distributed on the enzyme surface and more salt bridges present in hMDH compared with its nonhalophilic counterparts. Other features that contribute to the stabilization of thermophilic lactate dehydrogenase and thermophilic MDH-the incorporation of alanine into alpha helices and the introduction of negatively charged amino acids near their amino termini, both of which stabilize the alpha helix as a result of interaction with the positive part of the alpha-helix dipole-also were observed in hMDH.

The enzyme acetylcholinesterase generates a strong electrostatic field that can attract the cationic substrate acetylcholine to the active site. However, the long and narrow active site gorge seems inconsistent with the enzyme's high catalytic rate. A molecular dynamics simulation of acetylcholinesterase in water reveals the transient opening of a short channel, large enough to pass a water molecule, through a thin wall of the active site near tryptophan-84. This simulation suggests that substrate, products, or solvent could move through this "back door," in addition to the entrance revealed by the crystallographic structure. Electrostatic calculations show a strong field at the back door, oriented to attract the substrate and the reaction product choline and to repel the other reaction product, acetate. Analysis of the open back door conformation suggests a mutation that could seal the back door and thus test the hypothesis that thermal motion of this enzyme may open multiple routes of access to its active site.

Since the Protein Data Bank (PDB) inaugurated the “Layered Release Protocol” on 9 July 1998 (F. E. Bloom, “Policy Change,” Science 's Compass, 10 July, p. [175][1]) ([www.pdb.bnl.gov/][2] and [www2.ebi.ac.uk/pdb][3]), results have exceeded our highest expectations. Specifically, since July we have received 931 new entries, of which 813 were submitted by means of our latest data deposition software (AutoDep 2.1), which allows for “release on publication.” For less than 22% of these, “on-hold” is requested, and the rest have been either immediately released or held until publication (see [table][4] below for details). This is in sharp contrast to the situation just a year ago, when more than 75% of new entries were requested to be put “on-hold” for 1 year. View this table: This is an enormous tribute to the journals that have set the new policy requiring “Release on Publication,” as well as to the PDB, which instituted the “Layered Release Protocol,” making it possible to access data concurrently with publication. It is clear that there has been a profound change in the attitude of the vast majority of experimental crystallographers and nuclear magnetic resonance spectroscopists toward releasing their data either immediately or at the time of publication. This is an exciting development for structural biology that will have a positive impact on other scientific disciplines, industrial research, and education. [1]: /lookup/doi/10.1126/science.281.5374.175c [2]: http://www.pdb.bnl.gov/ [3]: http://www2.ebi.ac.uk/pdb [4]: #T1

For several years, Science policy has required that published X-ray crystallographic coordinates be deposited with a publically accessible database (e.g., Brookhaven Protein Data Bank). That policy recognized the high costs and risks of solving important structures to accord those who have made such investments successfully the time to reap their intellectual benefits. Wlodawer et al. (below) assert that recent technical enhancements have reduced “the time needed to solve a structure (to less than) than the allowed hold period” and have called for immediate release of the data. In cooperative discussions with our colleagues at Nature and other journals, Science wishes to evaluate how best to fulfill our responsibilities to the community. We urge readers to respond to a survey now underway (see ) and to us, so that future policy may be modified on the basis of scientific judgement. # Immediate Release of Crystallographic Data: A Proposal {#article-title-2} There has been an incredibly rapid increase in the rate of determination of three-dimensional (3D) structures of biomacromolecules, as reflected by the deposition of a new structure in the Protein Data Bank (PDB) at the Brookhaven National Laboratory ([1][1]), on average, every 5 hours. Unfortunately, in parallel, an increasing proportion of depositors take advantage of the PDB's policy of allowing structures to be kept “on hold” for up to a year after coordinate deposition. Despite a recent drop in the number of structures put “on hold,” nearly half the entries deposited are not released immediately. The policy of the PDB is based on rules drawn up by the International Union of Crystallography (IUCr) in the late 1980s for papers published in IUCr journals. These rules ([2][2]) also provide the basis for the policies of most other scientific journals and of a number of government funding agencies, such as the National Institutes of Health, for work undertaken with grant support. It is time to consider whether this policy is still appropriate. When it was debated and accepted by the community 10 years ago, the time needed to solve a macromolecular structure was often measured in years and was rarely less than 1 year. The time needed for detailed analysis of such structures was also fairly long. The 1-year hold on coordinates was therefore instituted to allow the authors to reap the fruit of their tremendous investment of time and effort. Because of recent advances in protein expression and purification, crystallization procedures, x-ray instrumentation, and computer software, the time needed to solve a structure is often shorter than the allowed hold period. In light of such developments, it is difficult to justify withholding coordinates for any period once the paper has been published. Biomolecular structure analysis has succeeded in bringing 3D structures to the forefront of molecular biological research. This success has expanded both the interest in and utility of the information being deposited in the PDB. The molecular modeling community has grown and evolved considerably, due to the expansion of this source of experimental data. The value of the data rests in their availability to the broader community. Methods are continuously being developed to analyze new structures and their relationships to the collection of existing structures. New uses for these data, such as statistical potentials for folding and threading calculations, and interface recognition tools, are evolving rapidly. No single research group can fully exhaust this wealth of information. The value of the resource grows proportionally to the timeliness of the data and to the number of scientists who have access to them. Three-dimensional structural information is also a crucial link elucidating the role of a translated region of a DNA sequence of unknown function. The time has come to change the rules of deposition so as to ensure that the coordinates are released concomitantly with publication of the paper (or papers) describing the structure. We are convinced that without access to the coordinates, the structures cannot be used for comparison with other proteins, for theoretical analysis or, more and more important, for drug design. We propose that coordinates deposited at the PDB should be marked as either “for immediate release” or “to be released upon publication.” We also recommend that the maximum hold for primary data (that is, x-ray structure factors, and nuclear magnetic resonance proton-proton distance and dihedral angle restraints) be reduced from 4 years to 1 year. The PDB is already working on a “layered approach” to deposition so that it will be possible to release entries as submitted, after the authors have checked for outliers and errors through the PDB's WEB-based AutoDep procedure, on the same day that they are deposited (with the permission of authors), or when the article related to the structure is published, if the authors request “release on publication date” rather than “hold for a year.” It is clear that such a change in policy will require cooperation of both the granting agencies and the scientific journals, as well as the overwhelming support of the scientists doing the research. It should be stressed that even the current policy is not uniformly enforced. These changes would bring macromolecular crystallography into line with the requirements of other fields, such as gene sequencing, which have never allowed extended hold periods. We hope that this proposed change in the deposition policy will be publicly debated and ultimately accepted. 1. [↵][3] . 2. [↵][4]International Union of Crystallography, Acta Crystallogr. A45, 658 (1989). [OpenUrl][5] [1]: #ref-1 [2]: #ref-2 [3]: #xref-ref-1-1 "View reference 1 in text" [4]: #xref-ref-2-1 "View reference 2 in text" [5]: {openurl}?query=rft.jtitle%253DActa%2BCrystallogr.%26rft.volume%253DA45%26rft.spage%253D658%26rft.atitle%253DACTA%2BCRYSTALLOGR%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx

A survey of all available double-stranded RNA crystal structures shows that there is a considerable range of variation in local conformation of a given base-pair doublet, but that there is no significant correlation between base-pair sequence and RNA local conformation.