Patrick Umbach - Academia.edu (original) (raw)
Papers by Patrick Umbach
Acta Crystallographica Section D-biological Crystallography, Nov 1, 1997
Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme s... more Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme solutions when varying the concentration of (NH4)2SO 4 and NaC1 for screening the repulsive forces between the monomers. At the initial aggregation stages clusters, which can be classified as mass-fractals undergoing diffusion limitedlike aggregation, coexist with monomers or small lysozyme oligomers. The kinetics of fractal growth deliver observables that exhibit distinct tendencies when examined as a function of the concentration and nature of the electrolyte. The behaviour of the observables changes drastically above 0.84M (NH4)2SO 4 and 0.60M NaCl. Static light scattering revealed a progressive restructuring of the fractals to compact structures at the latter stages of the reaction. Based on the correlations between the various observables an attempt is made to predict the long-term fate of the nucleating solutions.
GBM Annual Fall meeting M�nster 2004, Sep 1, 2004
Acta Crystallographica Section A, Aug 6, 2002
Journal of the American Chemical Society, 1996
Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. ... more Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. Am. Chem. Soc. 1995, 117, 9314-9322]. YANNIS GEORGALIS,* JENS SCHÜ LER, PATRICK UMBACH, AND WOLFRAM SAENGER Due to a mistake in a program performing the linear regression to the ln K versus 1/T data we have obtained values for the free entropy, ∆S) 0.405 (0.016 kJ mol-1 K-1 , of nucleation from intercepts that were twice divided by a factor of 10 3 while converting J to kJ. We have therefore erroneously concluded that the product-T m ∆S is negligible compared to ∆H. The value of the free energy of nucleation is overestimated by a factor of 1.8; it should read ∆G)-227 kJ/mol. Figure 4 of our paper should then be modified accordingly, i.e., the y-axis should extend from-317 to 317 rather than-160 to 160. Also in error by the same factor is the ∆∆G value that typifies the crystallization-dissolution process. It should read ∆∆G) 52 kJ mol-1. All other conclusions remain unaffected.
Acta Crystallographica Section D-biological Crystallography, Nov 1, 1997
Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme s... more Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme solutions when varying the concentration of (NH4)2SO 4 and NaC1 for screening the repulsive forces between the monomers. At the initial aggregation stages clusters, which can be classified as mass-fractals undergoing diffusion limitedlike aggregation, coexist with monomers or small lysozyme oligomers. The kinetics of fractal growth deliver observables that exhibit distinct tendencies when examined as a function of the concentration and nature of the electrolyte. The behaviour of the observables changes drastically above 0.84M (NH4)2SO 4 and 0.60M NaCl. Static light scattering revealed a progressive restructuring of the fractals to compact structures at the latter stages of the reaction. Based on the correlations between the various observables an attempt is made to predict the long-term fate of the nucleating solutions.
Journal of the American Chemical Society, Mar 1, 1998
Journal of the American Chemical Society, Sep 1, 1995
Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. ... more Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. Am. Chem. Soc. 1995, 117, 9314-9322]. YANNIS GEORGALIS,* JENS SCHÜ LER, PATRICK UMBACH, AND WOLFRAM SAENGER Due to a mistake in a program performing the linear regression to the ln K versus 1/T data we have obtained values for the free entropy, ∆S) 0.405 (0.016 kJ mol-1 K-1 , of nucleation from intercepts that were twice divided by a factor of 10 3 while converting J to kJ. We have therefore erroneously concluded that the product-T m ∆S is negligible compared to ∆H. The value of the free energy of nucleation is overestimated by a factor of 1.8; it should read ∆G)-227 kJ/mol. Figure 4 of our paper should then be modified accordingly, i.e., the y-axis should extend from-317 to 317 rather than-160 to 160. Also in error by the same factor is the ∆∆G value that typifies the crystallization-dissolution process. It should read ∆∆G) 52 kJ mol-1. All other conclusions remain unaffected.
Journal of the American Chemical Society, 1996
The initial crystallization phase of native and dimethylated β-cyclodextrins (β-CD) was investiga... more The initial crystallization phase of native and dimethylated β-cyclodextrins (β-CD) was investigated with small-angle static light scattering. Following simple considerations, one can obtain the crystallization exponent, predicted by the Avrami theory, from temperature quenching experiments. We found that a single-step mechanism, in accordance with the classical theory, holds for the crystal formation of native β-cyclodextrin. The crystal formation mechanism of the heptakis(2,6)-di-O-methyl)-β-CD is more complex, and involves a fast and a slow process. The exponents determined for each process indicate that crystallization starts with the formation of spherical clusters which aggregate further to form rod-shaped macrocrystals, in accordance with microscopic observations. In either case the determined exponents depend on the initial cyclodextrin concentration.
Acta Crystallographica Section D-biological Crystallography, Mar 1, 1997
ABSTRACT
Journal of Chemical Physics, May 22, 1997
A comparitive study of the nanostructure evolving during aggregation of hen-egg white lysozyme in... more A comparitive study of the nanostructure evolving during aggregation of hen-egg white lysozyme in supersaturated solution was carried out by dynamic light scattering ͑DLS͒ and scanning force microscopy ͑SFM͒. Lysozyme aggregate ͑cluster͒ formation was observed in solution in the presence of NaCl, ͑NH 4 ͒ 2 SO 4 , and NaNO 3 as precipitating agents. The growth kinetics were examined by DLS and revealed fractal growth of the clusters with a fractal dimension of 1.8 obtained independently of the type of inert salt. Such behavior is typical for diffusion-limited cluster-cluster ͑DLCA͒ aggregation. Initial lysozyme cluster sizes were in the range of 12-35 nm. SFM images of individual lysozyme clusters at the liquid-solid interface were obtained in the presence of NaCl and NaNO 3 under crystallization conditions, and revealed cluster sizes in agreement with those determined by DLS. Extended domains of smaller sized clusters appeared on the mica surface after subjecting supersaturated lysozyme solutions to a dialysis step. The feasibility of DLS and SFM for monitoring the nano-and mesoscopic morphology of lysozyme aggregates in supersatured solutions and at the solid-liquid interface is discussed.
Journal of the American Chemical Society, May 21, 1998
The liquid−liquid coexistence region of aqueous lysozyme−NaCl solutions was examined by time-reso... more The liquid−liquid coexistence region of aqueous lysozyme−NaCl solutions was examined by time-resolved small-angle static light scattering and light microscopy. At the initial stages of the reaction scattered intensities peaked at finite scattering vectors as expected for globular domains growing under the influence of competing interactions. An oscillatory behavior of the mean domain radius is observed at later stages of the reaction as a function of time. Microscopic observations revealed domains undergoing correlated ripening with time and forming labyrinthine microstructure and microcrystals at later stages. Potentials of the mean force computations yield first qualitative insights into the effective pair interactions during the process. The behavior of the system can be understood qualitatively as spinodal decomposition followed by nucleation, leading to a modulated phase type of microstructure.
Journal of the American Chemical Society, Feb 13, 1999
The cluster formation in nucleating hen egg white lysozyme-NaCl solutions was studied by simultan... more The cluster formation in nucleating hen egg white lysozyme-NaCl solutions was studied by simultaneous static and dynamic light scattering. Angular dependence measurements of the total scattered intensity and of the average cluster diffusion coefficient revealed the appearance of pronounced structure factor peaks at the initial nucleation stages. Such peaks are characteristic for the ordering often observed in highly concentrated colloidal suspensions. Free-energy minimizations of 4-60 particles, that adequately model the lysozyme monomer, were performed by using the effective interaction potentials described in previous work (Soumpasis; Georgalis Biophys. J. 1997, 72, 2770). Both experiment and computations show formation of clusters with fractal morphology, compatible with the findings of the present and previous works.
Acta Crystallographica Section A Foundations of Crystallography, 2002
Protein structure factory, highthroughput structural biology, structural genomics, structural pro... more Protein structure factory, highthroughput structural biology, structural genomics, structural proteomics, bioinformatics
GBM Annual Fall meeting M�nster 2004, 2004
![Research paper thumbnail of Fluorierung von Cyanurchlorid und Tieftemperatur-Kristallstruktur von [(ClCN)3F]+ [AsF6]?](https://attachments.academia-assets.com/91495341/thumbnails/1.jpg)
](Zeitschrift f�r anorganische und allgemeine Chemie, 1994
Bei der Redaktion eingegangen am 30. Dezember 1993. Inhaltsiibersicht. Durch Tieftemperaturfluori... more Bei der Redaktion eingegangen am 30. Dezember 1993. Inhaltsiibersicht. Durch Tieftemperaturfluorierung von 0,076 (fur wesentliche Reflexionen, R, = 0,088, Rw = 0,079 Cyanurchlorid, (ClCN),, mit Fz/AsF5 in SOzF2-Liisung wurde (fur alle Reflexe). Die Fluorierung von festem (ClCN), mit [(CICN),F]+ [AsF,]-(1) in nahezu quantitativer Ausbeute dar-[NF,]' [Sb2Fl,]-im Molverhaltnis 1 : 2 lieferte NF,, CClF,, gestellt, aus SOz bei Raumtemperatur umkristallisiert und SbF3, N2 und Spuren an CF,. Eine qualitative Reihenfolge bedurch eine Tieftemperatur-Rontgenstrukturanalyse (-170 "C) zuglich der FPDE-Werte von NF4+ und (XCN),F+ (X = H, F, identifiziert: R 3c, trigonal, a = b = 10,4246(23) A , c = C1) wurde ab initio berechnet. 5,1850(24) A, V = 1429,1(4) AS, Z = 6, RF = 0,056, Rw = Fluorination of Cyanuric Chloride and Low-Temperature Crystal Structure of [(ClCN),F] +.
Accounts of Chemical Research, 2003
Facilities and methods for the high-throughput crystal structure analysis of human proteins are d... more Facilities and methods for the high-throughput crystal structure analysis of human proteins are described as recently established in the Protein Structure Factory, a Berlin-area structural genomics project. Genes encoding human proteins are expressed in either recombinant Escherichia coli or yeast (Saccharomyces cerevisiae or Pichia pastoris). To facilitate and standardize protein purification, the target proteins are produced with various tags for affinity chromatography. For high-throughput crystallization, a robotic station is being set up that has the capacity to handle 960 000 experiments simultaneously. The resulting protein crystals will be subjected to X-ray diffraction experiments at the third-generation synchrotron storage ring BESSY where protein crystallography beamlines are currently under construction. The Protein Structure Factory's strategy for high-throughput production and structure analysis of human proteins is evaluated based on first results.
Acta Crystallographica Section D-biological Crystallography, Nov 1, 1997
Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme s... more Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme solutions when varying the concentration of (NH4)2SO 4 and NaC1 for screening the repulsive forces between the monomers. At the initial aggregation stages clusters, which can be classified as mass-fractals undergoing diffusion limitedlike aggregation, coexist with monomers or small lysozyme oligomers. The kinetics of fractal growth deliver observables that exhibit distinct tendencies when examined as a function of the concentration and nature of the electrolyte. The behaviour of the observables changes drastically above 0.84M (NH4)2SO 4 and 0.60M NaCl. Static light scattering revealed a progressive restructuring of the fractals to compact structures at the latter stages of the reaction. Based on the correlations between the various observables an attempt is made to predict the long-term fate of the nucleating solutions.
GBM Annual Fall meeting M�nster 2004, Sep 1, 2004
Acta Crystallographica Section A, Aug 6, 2002
Journal of the American Chemical Society, 1996
Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. ... more Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. Am. Chem. Soc. 1995, 117, 9314-9322]. YANNIS GEORGALIS,* JENS SCHÜ LER, PATRICK UMBACH, AND WOLFRAM SAENGER Due to a mistake in a program performing the linear regression to the ln K versus 1/T data we have obtained values for the free entropy, ∆S) 0.405 (0.016 kJ mol-1 K-1 , of nucleation from intercepts that were twice divided by a factor of 10 3 while converting J to kJ. We have therefore erroneously concluded that the product-T m ∆S is negligible compared to ∆H. The value of the free energy of nucleation is overestimated by a factor of 1.8; it should read ∆G)-227 kJ/mol. Figure 4 of our paper should then be modified accordingly, i.e., the y-axis should extend from-317 to 317 rather than-160 to 160. Also in error by the same factor is the ∆∆G value that typifies the crystallization-dissolution process. It should read ∆∆G) 52 kJ mol-1. All other conclusions remain unaffected.
Acta Crystallographica Section D-biological Crystallography, Nov 1, 1997
Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme s... more Static and dynamic light scattering have been employed to investigate the behaviour of lysozyme solutions when varying the concentration of (NH4)2SO 4 and NaC1 for screening the repulsive forces between the monomers. At the initial aggregation stages clusters, which can be classified as mass-fractals undergoing diffusion limitedlike aggregation, coexist with monomers or small lysozyme oligomers. The kinetics of fractal growth deliver observables that exhibit distinct tendencies when examined as a function of the concentration and nature of the electrolyte. The behaviour of the observables changes drastically above 0.84M (NH4)2SO 4 and 0.60M NaCl. Static light scattering revealed a progressive restructuring of the fractals to compact structures at the latter stages of the reaction. Based on the correlations between the various observables an attempt is made to predict the long-term fate of the nucleating solutions.
Journal of the American Chemical Society, Mar 1, 1998
Journal of the American Chemical Society, Sep 1, 1995
Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. ... more Light-Scattering Studies on the Thermally Induced Crystallization Transition of-Cyclodextrin [J. Am. Chem. Soc. 1995, 117, 9314-9322]. YANNIS GEORGALIS,* JENS SCHÜ LER, PATRICK UMBACH, AND WOLFRAM SAENGER Due to a mistake in a program performing the linear regression to the ln K versus 1/T data we have obtained values for the free entropy, ∆S) 0.405 (0.016 kJ mol-1 K-1 , of nucleation from intercepts that were twice divided by a factor of 10 3 while converting J to kJ. We have therefore erroneously concluded that the product-T m ∆S is negligible compared to ∆H. The value of the free energy of nucleation is overestimated by a factor of 1.8; it should read ∆G)-227 kJ/mol. Figure 4 of our paper should then be modified accordingly, i.e., the y-axis should extend from-317 to 317 rather than-160 to 160. Also in error by the same factor is the ∆∆G value that typifies the crystallization-dissolution process. It should read ∆∆G) 52 kJ mol-1. All other conclusions remain unaffected.
Journal of the American Chemical Society, 1996
The initial crystallization phase of native and dimethylated β-cyclodextrins (β-CD) was investiga... more The initial crystallization phase of native and dimethylated β-cyclodextrins (β-CD) was investigated with small-angle static light scattering. Following simple considerations, one can obtain the crystallization exponent, predicted by the Avrami theory, from temperature quenching experiments. We found that a single-step mechanism, in accordance with the classical theory, holds for the crystal formation of native β-cyclodextrin. The crystal formation mechanism of the heptakis(2,6)-di-O-methyl)-β-CD is more complex, and involves a fast and a slow process. The exponents determined for each process indicate that crystallization starts with the formation of spherical clusters which aggregate further to form rod-shaped macrocrystals, in accordance with microscopic observations. In either case the determined exponents depend on the initial cyclodextrin concentration.
Acta Crystallographica Section D-biological Crystallography, Mar 1, 1997
ABSTRACT
Journal of Chemical Physics, May 22, 1997
A comparitive study of the nanostructure evolving during aggregation of hen-egg white lysozyme in... more A comparitive study of the nanostructure evolving during aggregation of hen-egg white lysozyme in supersaturated solution was carried out by dynamic light scattering ͑DLS͒ and scanning force microscopy ͑SFM͒. Lysozyme aggregate ͑cluster͒ formation was observed in solution in the presence of NaCl, ͑NH 4 ͒ 2 SO 4 , and NaNO 3 as precipitating agents. The growth kinetics were examined by DLS and revealed fractal growth of the clusters with a fractal dimension of 1.8 obtained independently of the type of inert salt. Such behavior is typical for diffusion-limited cluster-cluster ͑DLCA͒ aggregation. Initial lysozyme cluster sizes were in the range of 12-35 nm. SFM images of individual lysozyme clusters at the liquid-solid interface were obtained in the presence of NaCl and NaNO 3 under crystallization conditions, and revealed cluster sizes in agreement with those determined by DLS. Extended domains of smaller sized clusters appeared on the mica surface after subjecting supersaturated lysozyme solutions to a dialysis step. The feasibility of DLS and SFM for monitoring the nano-and mesoscopic morphology of lysozyme aggregates in supersatured solutions and at the solid-liquid interface is discussed.
Journal of the American Chemical Society, May 21, 1998
The liquid−liquid coexistence region of aqueous lysozyme−NaCl solutions was examined by time-reso... more The liquid−liquid coexistence region of aqueous lysozyme−NaCl solutions was examined by time-resolved small-angle static light scattering and light microscopy. At the initial stages of the reaction scattered intensities peaked at finite scattering vectors as expected for globular domains growing under the influence of competing interactions. An oscillatory behavior of the mean domain radius is observed at later stages of the reaction as a function of time. Microscopic observations revealed domains undergoing correlated ripening with time and forming labyrinthine microstructure and microcrystals at later stages. Potentials of the mean force computations yield first qualitative insights into the effective pair interactions during the process. The behavior of the system can be understood qualitatively as spinodal decomposition followed by nucleation, leading to a modulated phase type of microstructure.
Journal of the American Chemical Society, Feb 13, 1999
The cluster formation in nucleating hen egg white lysozyme-NaCl solutions was studied by simultan... more The cluster formation in nucleating hen egg white lysozyme-NaCl solutions was studied by simultaneous static and dynamic light scattering. Angular dependence measurements of the total scattered intensity and of the average cluster diffusion coefficient revealed the appearance of pronounced structure factor peaks at the initial nucleation stages. Such peaks are characteristic for the ordering often observed in highly concentrated colloidal suspensions. Free-energy minimizations of 4-60 particles, that adequately model the lysozyme monomer, were performed by using the effective interaction potentials described in previous work (Soumpasis; Georgalis Biophys. J. 1997, 72, 2770). Both experiment and computations show formation of clusters with fractal morphology, compatible with the findings of the present and previous works.
Acta Crystallographica Section A Foundations of Crystallography, 2002
Protein structure factory, highthroughput structural biology, structural genomics, structural pro... more Protein structure factory, highthroughput structural biology, structural genomics, structural proteomics, bioinformatics
GBM Annual Fall meeting M�nster 2004, 2004
Zeitschrift f�r anorganische und allgemeine Chemie, 1994
Bei der Redaktion eingegangen am 30. Dezember 1993. Inhaltsiibersicht. Durch Tieftemperaturfluori... more Bei der Redaktion eingegangen am 30. Dezember 1993. Inhaltsiibersicht. Durch Tieftemperaturfluorierung von 0,076 (fur wesentliche Reflexionen, R, = 0,088, Rw = 0,079 Cyanurchlorid, (ClCN),, mit Fz/AsF5 in SOzF2-Liisung wurde (fur alle Reflexe). Die Fluorierung von festem (ClCN), mit [(CICN),F]+ [AsF,]-(1) in nahezu quantitativer Ausbeute dar-[NF,]' [Sb2Fl,]-im Molverhaltnis 1 : 2 lieferte NF,, CClF,, gestellt, aus SOz bei Raumtemperatur umkristallisiert und SbF3, N2 und Spuren an CF,. Eine qualitative Reihenfolge bedurch eine Tieftemperatur-Rontgenstrukturanalyse (-170 "C) zuglich der FPDE-Werte von NF4+ und (XCN),F+ (X = H, F, identifiziert: R 3c, trigonal, a = b = 10,4246(23) A , c = C1) wurde ab initio berechnet. 5,1850(24) A, V = 1429,1(4) AS, Z = 6, RF = 0,056, Rw = Fluorination of Cyanuric Chloride and Low-Temperature Crystal Structure of [(ClCN),F] +.
Accounts of Chemical Research, 2003
Facilities and methods for the high-throughput crystal structure analysis of human proteins are d... more Facilities and methods for the high-throughput crystal structure analysis of human proteins are described as recently established in the Protein Structure Factory, a Berlin-area structural genomics project. Genes encoding human proteins are expressed in either recombinant Escherichia coli or yeast (Saccharomyces cerevisiae or Pichia pastoris). To facilitate and standardize protein purification, the target proteins are produced with various tags for affinity chromatography. For high-throughput crystallization, a robotic station is being set up that has the capacity to handle 960 000 experiments simultaneously. The resulting protein crystals will be subjected to X-ray diffraction experiments at the third-generation synchrotron storage ring BESSY where protein crystallography beamlines are currently under construction. The Protein Structure Factory's strategy for high-throughput production and structure analysis of human proteins is evaluated based on first results.