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  • 1
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    The role of DNA shape in protein-DNA recognition (2009)
    Nature Publishing Group (NPG)
    Details
    Publication Date: 2009-10-30
    Description: The recognition of specific DNA sequences by proteins is thought to depend on two types of mechanism: one that involves the formation of hydrogen bonds with specific bases, primarily in the major groove, and one involving sequence-dependent deformations of the DNA helix. By comprehensively analysing the three-dimensional structures of protein-DNA complexes, here we show that the binding of arginine residues to narrow minor grooves is a widely used mode for protein-DNA recognition. This readout mechanism exploits the phenomenon that narrow minor grooves strongly enhance the negative electrostatic potential of the DNA. The nucleosome core particle offers a prominent example of this effect. Minor-groove narrowing is often associated with the presence of A-tracts, AT-rich sequences that exclude the flexible TpA step. These findings indicate that the ability to detect local variations in DNA shape and electrostatic potential is a general mechanism that enables proteins to use information in the minor groove, which otherwise offers few opportunities for the formation of base-specific hydrogen bonds, to achieve DNA-binding specificity.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793086/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2793086/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Rohs, Remo -- West, Sean M -- Sosinsky, Alona -- Liu, Peng -- Mann, Richard S -- Honig, Barry -- GM54510/GM/NIGMS NIH HHS/ -- R01 GM030518/GM/NIGMS NIH HHS/ -- U54 CA121852/CA/NCI NIH HHS/ -- U54 CA121852-05/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- England -- Nature. 2009 Oct 29;461(7268):1248-53. doi: 10.1038/nature08473.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Howard Hughes Medical Institute, Center for Computational Biology and Bioinformatics, Department of Biochemistry and Molecular Biophysics, Columbia University, 1130 Saint Nicholas Avenue, New York, New York 10032, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/19865164" target="_blank"〉PubMed〈/a〉
    Keywords: AT Rich Sequence/genetics ; Animals ; Arginine/metabolism ; Base Sequence ; DNA/*chemistry/genetics/*metabolism ; DNA-Binding Proteins/chemistry/*metabolism ; Databases, Factual ; Hydrogen Bonding ; Lysine ; *Nucleic Acid Conformation ; Nucleosomes/chemistry/metabolism ; Protein Binding ; Saccharomyces cerevisiae ; Static Electricity
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Nature Publishing Group (NPG)
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  • 2
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    Regenerating WIMPs in the light of direct and indirect detection (2012)
    American Physical Society (APS)
    Details
    Publication Date: 2012-09-18
    Description: Author(s): A. J. Williams, C. Bœhm, S. M. West, and D. Albornoz Vásquez There are several ways to explain the dark matter relic density other than by the ordinary freeze-out scenario. For example, the freeze-in mechanism may constitute an alternative for generating the correct relic density for dark matter candidates whose predicted freeze-out abundance is too low due t... [Phys. Rev. D 86, 055018] Published Mon Sep 17, 2012
    Keywords: Beyond the standard model
    Print ISSN: 0556-2821
    Electronic ISSN: 1089-4918
    Topics: Physics
    Published by American Physical Society (APS)
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  • 3
    Electronic Resource
    Electronic Resource
    Media engineering (1997)
    Springer
    BT technology journal 15 (1997), S. 83-93 
    Details
    ISSN: 1573-1995
    Source: Springer Online Journal Archives 1860-2000
    Topics: Electrical Engineering, Measurement and Control Technology
    Notes: Abstract Modern computer networks are capable of presenting a user with huge amounts of information. If an end user is unable or unwilling to assimilate what is available then it is of little value. The key contention in this paper is that information has to be engineered, just like any other product, if it is to deliver to its potential. Presented here is a systematic approach to the design and build of information-rich systems that has been designated media engineering.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1023/A:1018636824664
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    Paper (German National Licenses)
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  • 4
    Electronic Resource
    Electronic Resource
    Improved protein refolding using hollow-fibre membrane dialysis (1998)
    New York, NY [u.a.] : Wiley-Blackwell
    Biotechnology and Bioengineering 57 (1998), S. 590-599 
    Details
    ISSN: 0006-3592
    Keywords: protein refolding ; hollow-fibre membrane ; dialysis ; carbonic anhydrase ; Chemistry ; Biochemistry and Biotechnology
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology , Process Engineering, Biotechnology, Nutrition Technology
    Notes: We have used a cellulose acetate, hollow-fibre (HF) ultrafiltration membrane to refold bovine carbonic anhydrase, loaded into the lumen space, by removing the denaturant through controlled dialysis via the shell side space. When challenged with GdnHCl-denatured carbonic anhydrase, 70% of the loaded protein reptated through the membrane into the circulating dialysis buffer. Reptation occurred because the protein, in its fully unfolded configuration, was able to pass through the pores. The loss of carbonic anhydrase through the membrane was controlled by the dialysis conditions. Dialysis against 0.05 M Tris-HCl for 30 min reduced the denaturant around the protein to a concentration that allowed the return of secondary structure, increasing the hydrodynamic radius, thus preventing protein transmission. Under these conditions a maximum of 42% of carbonic anhydrase was recovered (from a starting concentration of 5 mg/mL) with 94% activity. This is an improvement over refolding carbonic anhydrase by simple batch dilution, which gave a maximum reactivation of 85% with 35% soluble protein yield. The batch refolding of carbonic anhydrase is very sensitive to temperature; however, during HF refolding between 0 and 25°C the temperature sensitivity was considerably reduced. In order to reduce the convection forces that give rise to aggregation and promote refolding the dialyzate was slowly heated from 4 to 25°C. This slow, temperature-controlled refolding gave an improved soluble protein recovery of 55% with a reactivation yield of 90%. The effect of a number of additives on the refolding system performance were tested: the presence of PEG improved both the protein recovery and the recovered activity from the membrane, while the detergents Tween 20 and IGEPAL CA-630 increased only the refolding yield. ©1998 John Wiley & Sons, Inc. Biotechnol Bioeng 57: 590-599, 1998.
    Additional Material: 8 Ill.
    Type of Medium: Electronic Resource
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    Paper (German National Licenses)
  • 5
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    Characterization of functional and phenotypic changes in anti-Gag vaccine-induced T cell responses and their role in protection after HIV-1 infection (2005)
    National Academy of Sciences
    Details
    Publication Date: 2005-03-07
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 6
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    Regenerating WIMPs in the light of direct and indirect detection (2012)
    American Physical Society
    Details
    Publication Date: 2012-09-17
    Print ISSN: 1550-7998
    Electronic ISSN: 1550-2368
    Topics: Physics
    Published by American Physical Society
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