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  • 1
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    Design of a switchable eliminase [Biophysics and Computational Biology] (2011)
    National Academy of Sciences
    Details
    Publication Date: 2011-04-27
    Description: The active sites of enzymes are lined with side chains whose dynamic, geometric, and chemical properties have been finely tuned relative to the corresponding residues in water. For example, the carboxylates of glutamate and aspartate are weakly basic in water but become strongly basic when dehydrated in enzymatic sites. The dehydration of the carboxylate, although intrinsically thermodynamically unfavorable, is achieved by harnessing the free energy of folding and substrate binding to reach the required basicity. Allosterically regulated enzymes additionally rely on the free energy of ligand binding to stabilize the protein in a catalytically competent state. We demonstrate the interplay of protein folding energetics and functional group tuning to convert calmodulin (CaM), a regulatory binding protein, into AlleyCat, an allosterically controlled eliminase. Upon binding Ca(II), native CaM opens a hydrophobic pocket on each of its domains. We computationally identified a mutant that (i) accommodates carboxylate as a general base within these pockets, (ii) interacts productively in the Michaelis complex with the substrate, and (iii) stabilizes the transition state for the reaction. Remarkably, a single mutation of an apolar residue at the bottom of an otherwise hydrophobic cavity confers catalytic activity on calmodulin. AlleyCat showed the expected pH-rate profile, and it was inactivated by mutation of its active site Glu to Gln. A variety of control mutants demonstrated the specificity of the design. The activity of this minimal 75-residue allosterically regulated catalyst is similar to that obtained using more elaborate computational approaches to redesign complex enzymes to catalyze the Kemp elimination reaction.
    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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  • 2
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    An antibody binding site on cytochrome c defined by hydrogen exchange and two-dimensional NMR (1990)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1990-08-17
    Description: The interaction of a protein antigen, horse cytochrome c (cyt c), with a monoclonal antibody has been studied by hydrogen-deuterium (H-D) exchange labeling and two-dimensional nuclear magnetic resonance (2D NMR) methods. The H-exchange rate of residues in three discontiguous regions of the cyt c polypeptide backbone was slowed by factors up to 340-fold in the antibody-antigen complex compared with free cyt c. The protected residues, 36 to 38, 59, 60, 64 to 67, 100, and 101, and their hydrogen-bond acceptors, are brought together in the three-dimensional structure to form a contiguous, largely exposed protein surface with an area of about 750 square angstroms. The interaction site determined in this way is consistent with prior epitope mapping studies and includes several residues that were not previously identified. The hydrogen exchange labeling approach can be used to map binding sites on small proteins in antibody-antigen complexes and may be applicable to protein-protein and protein-ligand interactions in general.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3432411/" 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/PMC3432411/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Paterson, Y -- Englander, S W -- Roder, H -- GM 31847/GM/NIGMS NIH HHS/ -- GM 35926/GM/NIGMS NIH HHS/ -- R01 GM031847/GM/NIGMS NIH HHS/ -- S07-RR-05415-28/RR/NCRR NIH HHS/ -- New York, N.Y. -- Science. 1990 Aug 17;249(4970):755-9.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Microbiology, University of Pennsylvania, Philadelphia 19104.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/1697101" target="_blank"〉PubMed〈/a〉
    Keywords: Antibodies, Monoclonal/immunology/metabolism ; Antigen-Antibody Complex ; *Binding Sites, Antibody ; Chemical Phenomena ; Chemistry ; Cytochrome c Group/*immunology ; Deuterium ; Epitopes/immunology ; Hydrogen/*metabolism ; Hydrogen Bonding ; Kinetics ; *Magnetic Resonance Spectroscopy ; Molecular Structure ; Protein Conformation
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 3
    Electronic Resource
    Electronic Resource
    Relayed magnetization transfer by isotropic mixing in exchanging systems
    Amsterdam : Elsevier
    Journal of Magnetic Resonance (1969) 78 (1988), S. 597-602 
    Details
    ISSN: 0022-2364
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1016/0022-2364(88)90146-1
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  • 4
    Electronic Resource
    Electronic Resource
    Photometrische Bestimmung von Quecksilber(II) im Nanogrammbereich mit Thio-Michlers Keton
    Amsterdam : Elsevier
    Talanta 24 (1977), S. 99-103 
    Details
    ISSN: 0039-9140
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0039-9140(77)80156-2
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  • 5
    Electronic Resource
    Electronic Resource
    Changing morphology of metallic monolayers via temperature controlled heteroepitaxial growth
    Amsterdam : Elsevier
    Surface Science 298 (1993), S. 121-126 
    Details
    ISSN: 0039-6028
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0039-6028(93)90088-2
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  • 6
    Electronic Resource
    Electronic Resource
    Structure and complete chemical passivation of Pt(997)
    Amsterdam : Elsevier
    Surface Science 297 (1993), S. 19-26 
    Details
    ISSN: 0039-6028
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0039-6028(93)90011-8
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  • 7
    Electronic Resource
    Electronic Resource
    On the possibility of phase separation in the extended Hubbard model
    Amsterdam : Elsevier
    Solid State Communications 76 (1990), S. 1333-1336 
    Details
    ISSN: 0038-1098
    Source: Elsevier Journal Backfiles on ScienceDirect 1907 - 2002
    Topics: Physics
    Type of Medium: Electronic Resource
    URL: http://linkinghub.elsevier.com/retrieve/pii/0038-1098(90)90380-T
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  • 8
    Electronic Resource
    Electronic Resource
    Radiative heat transfer in transient hot-wire measurements of thermal conductivity (1991)
    Springer
    International journal of thermophysics 12 (1991), S. 985-997 
    Details
    ISSN: 1572-9567
    Keywords: radiative heat transfer ; thermal conductivity ; toluene ; transient hot-wire technique
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract New measurements of the thermal conductivity of liquid toluene between 300 and 550 K have been used to study the importance of radiative heat transfer when using the transient hot-wire technique. The experimental data were used to obtain the radiation correction to the hot-wire temperature rises. Radiationcorrected values of thermal conductivity are reported. This study shows that the transient hot-wire method is much less affected by radiation than steady-state techniques.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00503514
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  • 9
    Electronic Resource
    Electronic Resource
    Thermal conductivity surface of argon: A fresh analysis (1991)
    Springer
    International journal of thermophysics 12 (1991), S. 965-984 
    Details
    ISSN: 1572-9567
    Keywords: argon ; liquid ; supercritical ; surface fit ; thermal conductivity ; transient hot wire technique ; vapor
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract This paper presents a fresh analysis of the thermal conductivity surface of argon at temperatures between 100 and 325 K with pressures up to 70 MPa. The new analysis is justified for several reasons. First, we discovered an error in the compression-work correction, which is applied when calculating thermal conductivity and thermal diffusivity obtained with the transient hot-wire technique. The effect of the error is limited to low densities, i.e., for argon below 5 mol·L−1. The error in question centers on the volume of fluid exposed to compression work. Once corrected, the low-density data agree very well with the available theory for both dilute-gas thermal conductivity and the first density coefficient of thermal conductivity. Further, the corrected low-density data, if used in conjunction with our previously reported data for the liquid and supercritical dense-gas phases, allow us to represent the thermal conductivity in the critical region with a recently developed mode-coupling theory. Thus the new surface incorporates theoretically based expressions for the dilute-gas thermal conductivity, the first density coefficient, and the critical enhancement. The new surface exhibits a significant reduction in overall error compared to our previous surface which was entirely empirical. The uncertainty in the new thermal conductivity surface is ±2.2% at the 95% confidence level.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00503513
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  • 10
    Electronic Resource
    Electronic Resource
    Thermal diffusivity measurement by the transient hot-wire technique: A reappraisal (1988)
    Springer
    International journal of thermophysics 9 (1988), S. 293-316 
    Details
    ISSN: 1572-9567
    Keywords: argon ; thermal conductivity ; thermal diffusivity ; toluene ; transient hot-wire technique ; m-xylene
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Notes: Abstract The theory of the transient hot-wire technique for thermal conductivity measurements is reassessed in the special context of thermal diffusivity measurements. A careful examination of the working equation and an error analysis are employed to identify the principal sources of error. Notwithstanding earlier claims to the contrary, the best precision that can be attained in thermal diffusivity measurements is of the order of ±3%, while the accuracy is inevitably poorer. Experimental evidence is adduced from two different instruments that supports the analysis given here. Although the technique cannot yield values of the thermal diffusivity, k, as accurate as can be achieved by the use of the best possible individual values of λ,ρ, and C p in the relation k=λ/ρC p, the simplicity of the technique makes it attractive for many purposes. It is even possible to derive values of the isobaric heat capacity C p for many fluids not available from other methods.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00513073
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