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Franz X Schmid

Publications and source records attributed to Franz X Schmid.

At least 19 recordsLinked to original sources
PubMed2006

Key role of coulombic interactions for the folding transition state of the cold shock protein.

The cold shock protein CspB shows a five-stranded beta-sheet structure, and it folds rapidly via a native-like transition state. A previous Phi value analysis showed that most of the residues with Phi values close to one reside in strand beta1, and two of them, Lys5 and Lys7 are partially exposed charged residues. To elucidate how coulombic interactions of these two residues contribute to the energetic organisation of the folding transition state we performed comparative folding experiments in the presence of an ionic denaturant (guanidinium chloride) and a non-ionic denaturant (urea) and a double-mutant analysis. Lys5 contributes 6.6 kJ mol(-1) to the stability of the transition state, and half of it originates from screenable coulombic interactions. Lys7 contributes 5.3 kJ mol(-1), and 3.4 kJ mol(-1) of it are screened by salt. In the folded protein Lys7 interacts with Asp25, and the screenable coulombic interaction between these two residues is fully formed in the transition state. This suggests that long-range coulombic interactions such as those originating from Lys5 and Lys7 of CspB can be important for organizing and stabilizing native-like structure early in protein folding.

Bacterial Proteins↗
PubMed2006

In vitro evolution of a hyperstable Gbeta1 variant.

An in-vitro selection strategy was used to obtain strongly stabilized variants of the beta1 domain of protein G (Gbeta1). In a two-step approach, first candidate positions with a high potential for stabilization were identified in Gbeta1 libraries that were created by error-prone PCR, and then, after randomization of these positions by saturation mutagenesis, strongly stabilized variants were selected. For both steps the in-vitro selection method Proside was employed. Proside links the stability of a protein with the infectivity of a filamentous phage. Ultimately, residues from the two best selected variants were combined in a single Gbeta1 molecule. This variant with the four mutations E15V, T16L, T18I, and N37L showed an increase of 35.1 degrees C in the transition midpoint and of 28.5 kJ mol(-1) (at 70 degrees C) in the Gibbs free energy of stabilization. It was considerably more stable than the best variant from a previous Proside selection, in which positions were randomized that had originally been identified by computational design. Only a single substitution (T18I) was found in both selections. The best variants from the present selection showed a higher cooperativity of thermal unfolding, as indicated by an increase in the enthalpy of unfolding by about 60 kJ mol(-1). This increase is apparently correlated with the presence of Leu residues that were selected at the positions 16 and 37.

Bacterial Proteins↗
PubMed2006

Specificity of the initial collapse in the folding of the cold shock protein.

The two-state folding reaction of the cold shock protein from Bacillus caldolyticus (Bc-Csp) is preceded by a rapid chain collapse. A fast shortening of intra-protein distances was revealed by Förster resonance energy transfer (FRET) measurements with protein variants that carried individual pairs of donor and acceptor chromophores at various positions along the polypeptide chain. Here we investigated the specificity of this rapid compaction. Energy transfer experiments that probed the stretching of strand beta2 and the close approach between the strands beta1 and beta2 revealed that the beta1-beta2 hairpin is barely formed in the collapsed form, although it is native-like in the folding transition state of Bc-Csp. The time course of the collapse could not be resolved by pressure or temperature jump experiments, indicating that the collapsed and extended forms are not separated by an energy barrier. The co-solute (NH4)2SO4 stabilizes both native Bc-Csp and the collapsed form, which suggests that the large hydrated SO4(2-) ions are excluded from the surface of the collapsed form in a similar fashion as they are excluded from folded Bc-Csp. Ethylene glycol increases the stability of proteins because it is excluded preferentially from the backbone, which is accessible in the unfolded state. The collapsed form of Bc-Csp resembles the unfolded form in its interaction with ethylene glycol, suggesting that in the collapsed form the backbone is still accessible to water and small molecules. Our results thus rule out that the collapsed form is a folding intermediate with native-like chain topology. It is better described as a mixture of compact conformations that belong to the unfolded state ensemble. However, some of its structural elements are reminiscent of the native protein.

Ammonium Sulfate↗
PubMed2006

The correlation between protein stability and dipole moment: a critical test.

Improving the stability of proteins is a major aim in basic and applied protein science. Querol and coworkers calculated changes in the quasi-electric dipole moment of a protein and used it as a simple criterion to predict stabilizing charge mutations. They employed this method to propose for the bacterial cold shock protein Bc-Csp a number of charge mutations that should have a strong influence on stability. We produced eight variants of Bc-Csp with such mutations and measured their stabilities experimentally. However, we could not find a correlation between the stability and the quasi dipole moment of these variants. Possibly, the quasi dipole moment reflects only a secondary aspect of the changes that are caused by charge mutations in a protein.

Bacterial Proteins↗
PubMed2005

A stable disulfide-free gene-3-protein of phage fd generated by in vitro evolution.

Disulfide bonds provide major contributions to the conformational stability of proteins, and their cleavage often leads to unfolding. The gene-3-protein of the filamentous phage fd contains two disulfides in its N1 domain and one in its N2 domain, and these three disulfide bonds are essential for the stability of this protein. Here, we employed in vitro evolution to generate a disulfide-free variant of the N1-N2 protein with a high conformational stability. The gene-3-protein is essential for the phage infectivity, and we exploited this requirement for a proteolytic selection of stabilized protein variants from phage libraries. First, optimal replacements for individual disulfide bonds were identified in libraries, in which the corresponding cysteine codons were randomized. Then stabilizing amino acid replacements at non-cysteine positions were selected from libraries that were created by error-prone PCR. This stepwise procedure led to variants of N1-N2 that are devoid of all three disulfide bonds but stable and functional. The best variant without disulfide bonds showed a much higher conformational stability than the disulfide-containing wild-type form of the gene-3-protein. Despite the loss of all three disulfide bonds, the midpoints of the thermal transitions were increased from 48.5 degrees C to 67.0 degrees C for the N2 domain and from 60.0 degrees C to 78.7 degrees C for the N1 domain. The major loss in conformational stability caused by the removal of the disulfides was thus over-compensated by strongly improved non-covalent interactions. The stabilized variants were less infectious than the wild-type protein, probably because the domain mobility was reduced. Only a small fraction of the sequence space could be accessed by using libraries created by error-prone PCR, but still many strongly stabilized variants could be identified. This is encouraging and indicates that proteins can be stabilized by mutations in many different ways.

Bacteriophage M13↗
PubMed2005

Evolutionary protein stabilization in comparison with computational design.

Two major strategies are currently used for stabilizing proteins: in vitro evolution and computational design. Here, we used gene libraries of the beta1 domain of the streptococcal protein G (Gbeta1) and Proside, an in vitro selection method, to identify stabilized variants of this protein. In the Gbeta1 libraries, the codons for the four boundary positions 16, 18, 25, and 29 were randomized. Many Gbeta1 variants with strongly increased thermal stabilities were found in 11 selections performed with five independent libraries. Previously, Mayo and co-workers used computational design to stabilize Gbeta1 by sequence optimization at the same positions. Their best variant ranked third within the panel of the selected variants. None of the ten computed sequences was found in the Proside selections, because several computed residues for positions 18 and 29 were not optimal for stability.

Bacterial Proteins↗
PubMed2005

Planimetry of mitral valve stenosis by magnetic resonance imaging.

OBJECTIVES: We sought to determine whether noninvasive planimetry of the mitral valve area (MVA) by magnetic resonance imaging (MRI) is feasible and reliable in patients with mitral stenosis (MS). BACKGROUND: Accurate assessment of MVA is particularly important for the management of patients with valvular stenosis. Current standard techniques for assessing the severity of MS include echocardiography (ECHO) and cardiac catheterization (CATH). METHODS: In 22 patients with suspected or known MS, planimetry of MVA was performed with a 1.5-T magnetic resonance scanner using a breath-hold balanced gradient echo sequence (true FISP). Data were compared with echocardiographically determined MVA (ECHO-MVA, n = 22), as well as with invasively calculated MVA by the Gorlin-formula at (CATH-MVA, n = 17). RESULTS: The correlation between MRI- and CATH-MVA was 0.89 (p < 0.0001), and the correlation between MRI- and ECHO-MVA was 0.81 (p < 0.0001). The MRI-MVA slightly overestimated CATH-MVA by 5.0% (1.60 +/- 0.45 cm(2) vs. 1.52 +/- 0.49 cm(2), p = NS) and ECHO-MVA by 8.1% (1.61 +/- 0.42 cm(2) vs. 1.48 +/- 0.42 cm(2), p < 0.05). On receiver-operating characteristic curve analysis, a value of MRI-MVA below 1.65 cm(2) indicated mitral stenosis (CATH-MVA < or =1.5 cm(2)), with a good sensitivity and specificity (89% and 75%, respectively). CONCLUSIONS: Magnetic resonance planimetry of the mitral valve orifice in mitral stenosis offers a reliable and safe method for noninvasive quantification of mitral stenosis. In the clinical management of patients with mitral stenosis, it has to be considered that planimetry by MRI slightly overestimates MVA, as compared with MVA calculated echocardiographically and at catheterization.

Aged↗
PubMed2005

Prolyl isomerization as a molecular timer in phage infection.

Prolyl cis-trans isomerizations are intrinsically slow reactions and known to be rate-limiting in many protein folding reactions. Here we report that a proline is used as a molecular timer in the infection of Escherichia coli cells by the filamentous phage fd. The phage is activated for infection by the disassembly of the two N-terminal domains, N1 and N2, of its gene-3-protein, which is located at the phage tip. Pro213, in the hinge between N1 and N2, sets a timer for the infective state. The timer is switched on by cis-to-trans and switched off by the unusually slow trans-to-cis isomerization of the Gln212-Pro213 peptide bond. The switching rate and thus the infectivity of the phage are determined by the local sequence around Pro213, and can be tuned by mutagenesis.

Bacteriophage M13↗
PubMed2005

Stabilization of the cold shock protein CspB from Bacillus subtilis by evolutionary optimization of Coulombic interactions.

The bacterial cold shock proteins (Csp) are used by both experimentalists and theoreticians as model systems for analyzing the Coulombic contributions to protein stability. We employ Proside, a method of directed evolution, to identify stabilized variants of Bs-CspB from Bacillus subtilis. Proside links the increased protease resistance of stabilized protein variants to the infectivity of a filamentous phage. Here, three cspB libraries were used for in vitro selections to explore the stabilizing potential of charged amino acids in Bs-CspB. In the first library codons for nine selected surface residues were partially randomized, in the second one random mutations were introduced non-specifically by error-prone PCR, and in the third one the spontaneous mutation rate of the phage in Escherichia coli was used. Stabilizing mutations were found at the surface positions 1, 3, 46, 48, 65, and 66. The contributions of these mutations to stability were characterized by analyzing them individually and in combination. The best combination (M1R, E3K, K65I, and E66L) increased the midpoint of thermal unfolding of Bs-CspB from 53.8 to 85.0 degrees C. The effects of most mutations are strongly context dependent. A good example is provided by the E3R mutation. It is strongly stabilizing (DeltaDeltaGD=11.1kJ mol(-1)) in the wild-type protein, but destabilizing (DeltaDeltaGD=-4.0kJ mol(-1)) in the A46K/S48R/E66L variant. The stabilizations by charge mutations did not correlate well with the corresponding changes in the protein net charge, and they could not be ascribed to the formation of ion pairs. Previous theoretical analyses did not identify the stabilization caused by the mutations at positions 1, 46, and 48. Also, electrostatics calculations based on protein net charge or charge asymmetry did not predict well the stability changes that occur when charged residues in Bs-CspB are mutated. It remains a challenge to model the Coulombic interactions of charged residues in a protein and to determine their contributions to the Gibbs free energy of protein folding.

Bacillus subtilis↗
PubMed2005

Cryopreservation of human endothelial cells for vascular tissue engineering.

To investigate the influence of cryopreservation on endothelial cell growth, morphology, and function human umbilical vein endothelial cells (HUVECs) were frozen following a standard protocol. Cell suspensions were exposed to 10% dimethyl sulfoxide in a high-potassium solution, cooled to -80 degrees C at 1 degrees C/min and stored in liquid nitrogen for 7-36 days. Samples were thawed in a 37 degrees C water bath and the cryoprotectant was removed by serial dilution. The growth of cell suspensions was assayed by culturing 7300 cells/cm2 for 3-5 days in order to determine the cell multiplication factor. Fresh and cryopreserved/thawed cells were analyzed for their growth, and their anti-inflammatory and anti-coagulant function by using cellular ELISA. Cryopreservation resulted in a retrieval of 66 +/- 5% and a viability of 79 +/- 3%. Cryopreserved/thawed and fresh cells showed identical doubling times and identical cell counts in the confluent monolayers. However, the lag phase of thawed HUVECs was approximately 36 h longer, resulting in significant differences in the cell multiplication factor at 3 and 5 days after seeding. After expansion to a sufficient cell count the lag phases were identical. Fresh and cryopreserved/thawed cells showed comparable anti-inflammatory and anti-coagulant activity, as judged by the basal and TNF-induced VCAM-1, ICAM-1, E-selectin, and thrombomodulin expression. Cryopreserved/thawed and recultivated endothelial cells are suitable for endothelialization of autologous allograft veins. Such tissue-engineered grafts will offer the necessary clinical safety for those patients who lack autologous material.

Cell Adhesion Molecules↗
PubMed2004

The folding transition state of the cold shock protein is strongly polarized.

The cold shock protein CspB from Bacillus subtilis consists of a three-stranded (beta1-beta3) and a two stranded (beta4-beta5) sheet, which form a closed beta barrel structure. CspB folds and unfolds rapidly in a two-state reaction, and the unfolded and the folded molecules interconvert with a time constant of 30 ms at the midpoint of the urea-induced transition (at 25 degrees C). The transition state of folding is native-like, as judged by the Tanford betaT value of > or =0.9. By using a mutational approach and Phi value analysis, we find that the folding transition state of CspB is energetically polarized. Despite the high betaT value, most Phi values are low. Values close to 1 were found for only a few residues, particularly in strand beta1 (Lys5, Val6, Lys7, Asn10). The interactions of the Asn10 side-chain with the backbone at positions 12 and 13 define the turn that connects the strands beta1 and beta2. Lys5 and Val6 in beta1 interact with residues in beta4, and their high Phi values indicate that an energetic linkage between beta1 and beta4 and thus between the two sheets exists already in the transition state. We compared our experimental Phi values with theoretical predictions of the folding pathway of cold shock proteins. Several of them suggest that the entire first sheet is formed in the transition state, and some identify the beta1-beta4 pairing as a crucial step in folding. Alternative paths that involve formation of the second sheet and beta3-beta5 pairing reactions were, however, suggested as well. The calculations gave coarse-grained pictures that are limited in resolution to the two sheets of CspB or to the elements of secondary structure. They did not identify the key residues with the high Phi values within these structural elements.

Bacillus subtilis↗
PubMed2004

Rapid collapse precedes the fast two-state folding of the cold shock protein.

The cold shock protein Bc-Csp folds very rapidly in a reaction that is well described by a kinetic two-state mechanism without intermediates. We measured the shortening of six intra-protein distances during folding by Förster resonance energy transfer (FRET) in combination with stopped-flow experiments. Single tryptophan residues were engineered into the protein as the donors, and single 5-(((acetylamino)ethyl)amino)naphthalene-1-sulfonate (AEDANS) residues were placed as the acceptors at solvent-exposed sites of Bc-Csp. Their R0 value of about 22 A was well suited for following distance changes during the folding of this protein with a high sensitivity. The mutagenesis and the labeling did not alter the refolding kinetics. The changes in energy transfer during folding were monitored by both donor and acceptor emission and reciprocal effects were found. In two cases the donor-acceptor distances were similar in the unfolded and the folded state and, as a consequence, the kinetic changes in energy transfer upon folding were very small. For four donor/acceptor pairs we found that > or =50% of the increase in energy transfer upon folding occurred prior to the rate-limiting step of folding. This reveals that about half of the shortening of the intra-molecular distances upon folding has occurred already before the rate-limiting step and suggests that the fast two-state folding reaction of Bc-Csp is preceded by a very rapid collapse.

Amino Acid Substitution↗
PubMed2004

Early regression of left ventricular hypertrophy after aortic valve replacement by the Ross procedure detected by cine MRI.

AIM: The primary objective of our study was to assess the time course of left ventricular remodeling after the Ross procedure with the use of cine magnetic resonance imaging (MRI). METHODS: In a prospective study, 10 patients with isolated aortic valve disease were examined prior to aortic valve surgery, as well as at early follow-up (mean 4 weeks) and at late follow-up (mean 8 months) after pulmonary autograft aortic valve replacement (Ross procedure). The heart was imaged with a 1.5 T MR scanner along the short and long axes using a breath-hold, electrocardiogram (ECG)-triggered, cine gradient-echo sequence (FLASH). Myocardial mass and ventricular function were assessed. RESULTS: After aortic valve replacement, left ventricular myocardial mass (LVM) decreased by 13% (261 +/- 74 g to 230 +/- 65 g, p < 0.05) in the early postoperative period and by a further 16% in the late postoperative period to 192 +/- 31 g (p < 0.05). In addition, left ventricular end-diastolic and end-systolic volumes decreased from preoperative 187 +/- 89 mL (LV EDV) and 73 +/- 59 mL (LV ESV) to 119 +/- 55 mL and 56 +/- 42 mL, respectively, in the early postoperative period. In the late postoperative period, there was a further decrease to 98 +/- 30 (p < 0.05) and 33 +/- 19 mL, respectively. Ejection fraction did not change markedly after surgery (preoperatively 61 +/- 13% vs. 56 +/- 14% postoperatively). Patients with leading aortic stenosis were characterized by predominant regression of LVM and patients with leading aortic regurgitation by predominant regression of LV EDV (each p < 0.05). CONCLUSION: Cine MRI allows accurate assessment of left ventricular structure and geometry before and after aortic valve replacement with pulmonary autograft and is very sensitive in detecting relatively small changes of left ventricular myocardial mass and volumes early after hemodynamic relief as well as during serial assessment.

Adult↗
PubMed2004

Assessment of left ventricular cardiac output by arterial thermodilution technique via a left atrial catheter in a patient on a right ventricular assist device.

Following heart transplantation (HTx) in a 49-year old male, the patient's haemodynamic situation deteriorated in the early postoperative period despite increasing doses of catecholamines. When transoesophageal echocardiography (TEE) showed a dilated right ventricle, but adequate left ventricular (LV) function, a right ventricular assist device (RVAD) was implanted to support the right ventricle of the failing graft. Evaluation of the resulting cardiac output (CO) of the left ventricle and, thus, assessment of the remaining right ventricular function in patients supported by a RVAD is of great clinical interest. In this situation, continuous measurement of LV function, enabling assessment of the remaining right ventricular function, can be performed by pulse contour analysis following initial calibration of the system by arterial thermodilution CO measurement via a left atrial catheter.

Arteries↗
PubMed2003

A proline switch controls folding and domain interactions in the gene-3-protein of the filamentous phage fd.

The amino-terminal domains N1 and N2 of the gene-3-protein of phage fd form a bilobal structural and functional entity that protrudes from the phage tip. Domain N2 initiates the infection of Escherichia coli by binding to the F pilus. This binding results in the dissociation of the two domains and allows N1 to interact with the TolA receptor at the cell surface. The refolding of the N1-N2 fragment begins with the folding of domain N1, which takes a few milliseconds, followed by the folding of domain N2, which is complete within five minutes. The subsequent domain assembly is unusually slow and shows a time-constant of 6200 s at 25 degrees C. We found that the rate of this reaction is controlled by the trans to cis isomerization of the Gln212-Pro213 bond in the hinge subdomain of N2, a region that provides many interactions between N1 and N2 in the gene-3-protein. The substitution of Pro213 by Gly accelerated domain association 30-fold and revealed that the folding of the two individual domains and their assembly are indeed sequential steps in the refolding of the gene-3-protein. In the course of infection, the domains must separate to expose the binding site for TolA on domain N1. The kinetic block of domain reassembly caused by Pro213 isomerization could ensure that after the initial binding of N2 to the F pilus the open state persists until N1 and TolA are close enough for their mutual interaction. Pro213 isomerization might thus serve as a slow conformational switch in the function of the gene-3-protein.

Bacteriophage M13↗
PubMed2003

The folding mechanism of a two-domain protein: folding kinetics and domain docking of the gene-3 protein of phage fd.

The gene-3 protein (G3P) of filamentous phages is essential for the infection of Escherichia coli. The carboxy-terminal domain anchors this protein in the phage coat, whereas the two amino-terminal domains N1 and N2 protrude from the phage surface. We analyzed the folding mechanism of the two-domain fragment N1-N2 of G3P (G3P(*)) and the interplay between folding and domain assembly. For this analysis, a variant of G3P(*) was used that contained four stabilizing mutations (IIHY-G3P(*)). The observed refolding kinetics extend from 10 ms to several hours. Domain N1 refolds very rapidly (with a time constant of 9.4 ms at 0.5 M guanidinium chloride, 25 degrees C) both as a part of IIHY-G3P(*) and as an isolated protein fragment. The refolding of domain N2 is slower and involves two reactions with time constants of seven seconds and 42 seconds. These folding reactions of the individual domains are followed by a very slow, spectroscopically silent docking process, which shows a time constant of 6200 seconds. This reaction was detected by a kinetic unfolding assay for native molecules. Before docking, N1 and N2 unfold fast and independently, after docking they unfold slowly in a correlated fashion. A high energy barrier is thus created by domain docking, which protects G3P kinetically against unfolding. The slow domain docking is possibly important for the infection of E.coli by the phage. Upon binding to the F pilus, the N2 domain separates from N1 and the binding site for TolA on domain N1 is exposed. Since domain reassembly is so slow, this binding site remains accessible until pilus retraction has brought N1 close to TolA on the bacterial surface.

Bacteriophage M13↗