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  • 1
    Publication Date: 2003-11-25
    Description: A major challenge of computational protein design is the creation of novel proteins with arbitrarily chosen three-dimensional structures. Here, we used a general computational strategy that iterates between sequence design and structure prediction to design a 93-residue alpha/beta protein called Top7 with a novel sequence and topology. Top7 was found experimentally to be folded and extremely stable, and the x-ray crystal structure of Top7 is similar (root mean square deviation equals 1.2 angstroms) to the design model. The ability to design a new protein fold makes possible the exploration of the large regions of the protein universe not yet observed in nature.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Kuhlman, Brian -- Dantas, Gautam -- Ireton, Gregory C -- Varani, Gabriele -- Stoddard, Barry L -- Baker, David -- New York, N.Y. -- Science. 2003 Nov 21;302(5649):1364-8.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/14631033" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Circular Dichroism ; Computational Biology ; Computer Graphics ; Computer Simulation ; Crystallization ; Crystallography, X-Ray ; Databases, Protein ; Models, Molecular ; Molecular Sequence Data ; Monte Carlo Method ; Nuclear Magnetic Resonance, Biomolecular ; *Protein Conformation ; Protein Denaturation ; *Protein Engineering ; *Protein Folding ; Protein Structure, Secondary ; Proteins/*chemistry ; *Software ; Solubility ; Temperature ; Thermodynamics
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 97 (1975), S. 728-736 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 100 (1978), S. 7219-7223 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 4
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 108 (1986), S. 7872-7873 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 96 (1974), S. 7123-7125 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 6
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 98 (1976), S. 7432-7433 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    s.l. : American Chemical Society
    Journal of the American Chemical Society 99 (1977), S. 6881-6884 
    ISSN: 1520-5126
    Source: ACS Legacy Archives
    Topics: Chemistry and Pharmacology
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Il nuovo cimento della Società Italiana di Fisica 6 (1985), S. 593-608 
    ISSN: 0392-6737
    Keywords: Chemical thermodynamics ; Molecular biophysics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Description / Table of Contents: Riassunto In questo lavoro è stata studiata l'interazione fra bromuro di etidio (EB) e DNA in soluzione acqua-metanolo a varie temperature. Si è trovato che l'energia libera di Gibbs associata al legame DNA-EB può essere ben descritta da una relazione lineare nella costante dielettrica della soluzione, come visto anche per altri alcoli. Il ruolo dell'entalpia e dell'entropia di legame è piú semplice se queste quantità sono ricavate isodielettricamente (ε = costance). Con questa procedura, inoltre, è possibile separare le proprietà del solvente dalle caratteristiche del legame DNA-EB mostrando con chiarezza la presenza d'interazioni idrofobiche.
    Abstract: Резюме Исследуется взаимодействие ДНК с бромистым этидием (EB) в присутствии метанола ири различных температурах. Найдено, что свободная энергия Гиббса в случае связи ДНК-ЕВ линейно зависит от диэлектрической постоянной раствора. Указанное свойство обнаружено и для других спиртов. При рассмотрении энтальпии и энтропии в случае связи ДНК-ЕВ установлено, что их роль становится довольно простой, если их изменение осушествляется изодиэлектрически (ε=const). С помощью этой методики можно отличитя свойства, обусловленные растворителем, от свойств, овусловлениых взаимодействием ДНК и ЕВ. Таким образом, можно установить наличие гидрофобного взаимодействия.
    Notes: Summary The interaction of DNA with the dye ethidium bromide (EB) has been investigated under the presence of methanol at varying temperatures. The Gibbs free energy associated with the DNA-EB binding is found to be well described by its linear dependence upon the dielectric constant of the solution, a property also found for other alcohols. When the enthalpy and entropy associated with the binding are considered, it is found that their role becomes rather simple if their evaluation is performed isodielectrically (ε=const). According to this procedure, the varying properties of the solvent can be separated from those of the interacting DNA and EB and the presence of hydrophobic interactions becomes then well established.
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  • 9
    Electronic Resource
    Electronic Resource
    Springer
    Il nuovo cimento della Società Italiana di Fisica 6 (1985), S. 618-630 
    ISSN: 0392-6737
    Keywords: Chemical thermodynamics ; Molecular biophysics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Description / Table of Contents: Riassunto Si è studiata la denaturazione isoterma del DNA da timo di vitello indotta dalla presenza di quattro alcoli semplici in soluzione. Sono state eseguite sia misure a 67.2 °C, temperatura alla quale la frazione denaturata senza alcoli vale circa 20%, che profili di ≪fusione≫ a temperature variabili. I risultati mostrano che, al crescere della concentrazione e del gruppo alchilico degli alcoli la denaturazione dapprima raggiunge un valore massimo e poi torna indietro. Questo comportamento, attribuito alle proprietà ≪insolite≫ dell'acqua come risulta anche da misure di compressibilità indica che gli effetti idrofobici ed elettrostatici intervengono in modo complicato.
    Abstract: Резюме Исследуется изотермическая денатурация DNA тимуса, индуцированная наличием моногидридных спиртов в растворе. Измерения проводятся при температуре 67.2 °C, при которой денатурация в присутствии спиртов составляет около 20%. Также регистрируются профили плавления при различных температурах. Полученные результаты показывают, что при увеличении концентрации мума, а затем убывает. Это поведение, приписываемое свойствам ≪необыкновенной≫ воды, что получено также из измерений сжимаемости, указывает, что гидрофобные и электростатические эффекты связаны сложным образом.
    Notes: Summary The isothermal denaturation of calf thymus DNA, induced by the presence of some monohydric alcohols in the solution, was investigated. Measurements were performed at a temperature (67.2°C) at which the denaturation, in the absence of alcohols, is about 20% and melting profiles at varying temperatures were also recorded. Results show that with increasing alcohol concentration and alkyl group size DNA denaturation first reaches a maximum and then falls back. This behaviour, ascribed to «unusual» water properties as inferred also from compressibility measurements, indicates that hydrophobic and electrostatic effects are connected in a complex way.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Il nuovo cimento della Società Italiana di Fisica 2 (1983), S. 1065-1074 
    ISSN: 0392-6737
    Keywords: Chemical thermodynamics ; Molecular biophysics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Physics
    Description / Table of Contents: Riassunto La determinazione delle costanti di equilibrio, come risulta per esempio dalla nota rappresentazione di Scatchard, può essere fortemente errata poiché il valore della risposta del ligando è spesso affetto da grande incertezza. Una causa frequente di questa incertezza deriva dall'uso di campioni che contengono piccole quantità di ligando libero oppure dalla dialisi di equilibrio che è spesso alterata dall'effetto Donnan, perdite di ligando, ecc. Da un'analisi di questo problema si ricava qui un metodo semplice che, nonostante gl'inconvenienti di cui sopra, permette di determinare con grande precisione i parametri di equilibrio.
    Abstract: Резюме Определение постоянныш равновесия может окаться ненадежным, так как обычно величины отклика литандов известны отклика литандов известны с большой неопределенностью. Общая причина этой неопределенности связана с использованием образцов, которые содержат малое количество свободных лигандов, или с равновесным диализом, который обычно родвергается влиянию эффекта Доннана, потерям красителя и др. Из анализа этой проблемы предлагается простая процедура, которая позволяет получить рараметры равновесия с большей точностью.
    Notes: Summary The determination of equilibrium constants, seen,e.g., in the usual Scatchard plots, may be highly inaccurate because generally the values of the bound-ligand response are known with large uncertainty. A common cause of this inaccuracy stems from the use of samples that contain small amounts of free ligand, hardly avoided, or from equilibrium dialysis which is generally affected by the Donnan effect, dye losses, etc. From an analysis of this problem a simple procedure is derived here, so that, in spite of the above drawbacks, the equilibrium parameters can be obtained with better precision.
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