| 1. |
- Lehtio, J., et al.
(författare)
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Alpha-amylase inhibitors selected from a combinatorial library of a cellulose binding domain scaffold
- 2000
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 41:3, s. 316-322
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Tidskriftsartikel (refereegranskat)abstract
- A disulfide bridge-constrained cellulose binding domain (CBD,) derived from the cellobiohydrolase Ce17A from Trichoderma reesei has been investigated for use in scaffold engineering to obtain novel binding proteins. The gene encoding the wild-type 36 aa CBDWT domain was first inserted into a phagemid vector and shown to be functionally displayed on M13 filamentous phage as a protein III fusion protein with retained cellulose binding activity. A combinatorial library comprising 46 million variants of the CBD domain was constructed through randomization of 11 positions located at the domain surface and distributed over three separate beta -sheets of the domain. Using the enzyme porcine alpha-amylase (PPA) as target in biopannings, two CBD variants showing selective binding to the enzyme were characterized. Reduction and iodoacetamide blocking of cysteine residues in selected CBD variants resulted in a loss of binding activity, indicating a conformation dependent binding. Interestingly, further studies showed that the selected CBD variants were capable of competing with the binding of the amylase inhibitor acarbose to the enzyme. In addition, the enzyme activity could be partially inhibited by addition of soluble protein, suggesting that the selected CBD variants bind to the active site of the enzyme.
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| 2. |
- Andersson, K, et al.
(författare)
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Kinetic characterization of the interaction of the Z-fragment of protein A with mouse-IgG3 in a volume in chemical space.
- 1999
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 37:3
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Tidskriftsartikel (refereegranskat)abstract
- The kinetic rate parameters for the interaction between a single domain analogue of staphylococcal protein A (Z) and a mouse-IgG3 monoclonal antibody (MAb) were measured in Hepes buffer with different chemical additives. Five buffer ingredients (pH, NaCl, DMSO, EDTA, and KSCN) were varied simultaneously in 16 experiments following a statistical experimental plan. The 16 buffers thus spanned a volume in chemical space. A mathematical model, using data from the buffer composition, was developed and used to predict apparent kinetic parameters in five new buffers within the spanned volume. Association and dissociation parameters were measured in the new buffers, and these agreed with the predicted values, indicating that the model was valid within the spanned volume. The pattern of variation of the kinetic parameters in relation to buffer composition was different for association and dissociation, such that pH influenced both association and dissociation and NaCl influenced only dissociation. This indicated that the recognition mechanism (association) and the stability of the formed complex (dissociation) involve different binding forces, which can be further investigated by kinetic studies in systematically varied buffers.
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| 3. |
- Berndt, Kurt D, et al.
(författare)
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Conformational sampling by NMR solution structures calculated with the program DIANA evaluated by comparison with long-time molecular dynamics calculations in explicit water
- 1996
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 24, s. 304-313
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Tidskriftsartikel (refereegranskat)abstract
- The NMR solution structure of bovine pancreatic trypsin inhibitor (BPTI) obtained by distance geometry calculations with the program DIANA is compared with groups of conformers generated by molecular dynamics (MD) simulations in explicit water at ambient temperature and pressure. The MD simulations started from a single conformer and were free or restrained either by the experimental NOE distance restraints or by time-averaged restraints; the groups of conformers were collected either in 10 ps intervals during 200 ps periods of simulation, or in 50 ps intervals during a 1 ns period of simulation. Overall, these comparisons show that the standard protein structure determination protocol with the program DIANA provides a picture of the protein structure that is in agreement with MD simulations using "realistic" potential functions over a nanosecond timescale. For well-constrained molecular regions there is a trend in the free MD simulation of duration 1 ns that the sampling of the conformation space is slightly increased relative to the DIANA calculations. In contrast, for surface-exposed side-chains that are less extensively constrained by the NMR data, the DIANA conformers tend to sample larger regions of conformational space than conformers selected from any of the MD trajectories. Additional insights into the behavior of surface side-chains come from comparison of the MD runs of 200 ps or 1 ns duration. In this time range the sampling of conformation space by the protein surface depends strongly on the length of the simulation, which indicates that significant side-chain transitions occur on the nanosecond timescale and that much longer simulations will be needed to obtain statistically significant data on side-chain dynamics.
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| 4. |
- Hargbo, Jeanette, et al.
(författare)
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Hidden Markov Models That Use Predicted Secondary Structures For Fold Recognition
- 1999
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 36:1, s. 68-76
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Tidskriftsartikel (refereegranskat)abstract
- There are many proteins that share the same fold but have no clear sequence similarity. To predict the structure of these proteins, so called protein fold recognition methods have been developed. During the last few years, improvements of protein fold recognition methods have been achieved through the use of predicted secondary structures (Rice and Eisenberg, J Mol Biol 1997;267:1026-1038), as well as by using multiple sequence alignments in the form of hidden Markov models (HMM) (Karplus et al., Proteins Suppl 1997;1:134-139). To test the performance of different fold recognition methods, we have developed a rigorous benchmark where representatives for all proteins of known structure are matched against each other. Using this benchmark, we have compared the performance of automatically-created hidden Markov models with standard-sequence-search methods. Further, we combine the use of predicted secondary structures and multiple sequence alignments into a combined method that performs better than methods that do not use this combination of information. Using only single sequences, the correct fold of a protein was detected for 10% of the test cases in our benchmark. Including multiple sequence information increased this number to 16%, and when predicted secondary structure information was included as well, the fold was correctly identified in 20% of the cases. Moreover, if the correct secondary structure was used, 27% of the proteins could be correctly matched to a fold. For comparison, blast2, fasta, and ssearch identifies the fold correctly in 13-17% of the cases. Thus, standard pairwise sequence search methods perform almost as well as hidden Markov models in our benchmark. This is probably because the automatically-created multiple sequence alignments used in this study do not contain enough diversity and because the current generation of hidden Markov models do not perform very well when built from a few sequences. Proteins 1999;36:68-76
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| 5. |
- Knapp, S, et al.
(författare)
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Thermal unfolding of small proteins with SH3 domain folding pattern
- 1998
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 31:3, s. 309-319
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Tidskriftsartikel (refereegranskat)abstract
- The thermal unfolding of three SH3 domains of the Tec family of tyrosine kinases was studied by differential scanning calorimetry and CD spectroscopy, The unfolding transition of the three protein domains in the acidic pH region can be described as a reversible two-state process. For all three SH3 domains maximum stability was observed in the pH region 4.5 < pH < 7.0 where these domains unfold at temperatures of 353K (Btk), 342K (Itk), and 344K (Tec), At these temperatures an enthalpy change of 196 kJ/mol, 178 kJ/mol, and 169 kJ/mol was measured for Btk-, Itk-, and Tec-SH3 domains, respectively. The determined changes in heat capacity between the native and the denatured state are in an usual range expected for small proteins. Our analysis revealed that all SH3 domains studied are only weakly stabilized and have free energies of unfolding which do not exceed 12-16 kJ/mol but show quite high melting temperatures. Comparing unfolding free energies measured for eukaryotic SH3 domains with those of the topologically identical Sso7d protein from the hyperthermophile Sulfolobus solfataricus, the increased melting temperature of the thermostable protein is due to a broadening as well as a significant lifting of its stability curve. However, at their physiological temperatures, 310K for mesophilic SH3 domains and 350K for Sso7d, eukaryotic SH3 domains and Sso7d show very similar stabilities. (C) 1998 Wiley-Liss, Inc.
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| 6. |
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| 7. |
- Schneider, Gisbert, et al.
(författare)
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Feature-extraction from endopeptidase cleavage sites in mitochondrial targeting peptides
- 1998
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Ingår i: Proteins. - 0887-3585 .- 1097-0134. ; 30:1, s. 49-60
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Tidskriftsartikel (refereegranskat)abstract
- Cleavage sites in nuclear-encoded mitochondrial protein targeting peptides (mTPs) from mammals, yeast, and plants have been analysed for characteristic physicochemical features using statistical methods, perceptrons, multilayer neural networks, and self-organizing feature maps, Three different sequence motifs were found, revealing loosely defined arginine motifs with Arg in positions -10, -3, and -2. A self-organizing feature map was able to cluster these three types of endopeptidase target sites but did not identify any species-specific characteristics in mTPs, Neural networks were used to define local sequence features around precursor cleavage sites.
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| 8. |
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| 9. |
- Agullo, Luis, et al.
(författare)
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Computational exploration of the binding mode of heme-dependent stimulators into the active catalytic domain of soluble guanylate cyclase
- 2016
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 84:10, s. 1534-1548
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Tidskriftsartikel (refereegranskat)abstract
- Soluble guanylate cyclase (sGC), the main target of nitric oxide (NO), has been proven to have a significant role in coronary artery disease, pulmonary hypertension, erectile dysfunction, and myocardial infarction. One of its agonists, BAY 41-2272 (Riociguat), has been recently approved for treatment of pulmonary arterial hypertension (PHA), while some others are in clinical phases of development. However, the location of the binding sites for the two known types of agonists, heme-dependent stimulators and heme-independent activators, is a matter of debate, particularly for the first group where both a location on the regulatory (H-NOX) and on the catalytic domain have been suggested by different authors. Here, we address its potential location on the catalytic domain, the unique well characterized at the structural level, by an in silico approach. Homology models of the catalytic domain of sGC in inactive or active conformations were constructed using the structure of previously described crystals of the catalytic domains of inactive sGCs (2WZ1, 3ET6) and of active adenylate cyclase (1CJU). Each model was submitted to six independent molecular dynamics simulations of about 1 s. Docking of YC-1, a classic heme-dependent stimulator, to all frames of representative trajectories of inactive and active conformations, followed by calculation of absolute binding free energies with the linear interaction energy (LIE) method, revealed a potential high-affinity binding site on the active structure. The site, located between the pseudo-symmetric and the catalytic site just over the loop (2)-(3), does not overlap with the forskolin binding site on adenylate cyclases.
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| 10. |
- Aifa, Sami, 1967-, et al.
(författare)
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Electrostatic interactions of peptides flanking the tyrosine kinase domain in the epidermal growth factor receptor provides a model for intracellular dimerization and autophosphorylation
- 2006
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 62:4, s. 1036-1043
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Tidskriftsartikel (refereegranskat)abstract
- The mechanism by which ligand-activated EGFR induces autophosphorylation via dimerization is not fully understood. Structural studies have revealed an extracellular loop mediated receptor dimerization. We have previously presented experimental data showing the involvement of a positive 13 amino acid peptide (R645-R657, P13+) from the intracellular juxtamembrane domain (JM) of EGFR important for intracellular dimerization and autophosphorylation. A model was presented that suggest that P13+ interacts with a negative peptide (D979-E991, P13-) positioned distal to the tyrosine kinase domain in the opposite EGFR monomer. The present work shows additional data strengthening this model. In fact, by analyzing protein sequences of 21 annotated ErbB proteins from 9 vertebrate genomes, we reveal the high conservation of peptides P13+ and P13- with regard to their sequence as well as their position relative to the tyrosine kinase (TK) domain. Moreover in silico structure modeling of these ErbB intracellular domains supports a general electrostatic P13+/P13- interaction, implying that the C-terminal of one receptor monomer is facing the TK domain of the other monomer in the receptor dimer and vice versa. This model provides new insights into the molecular mechanism of ErbB receptor activation and suggests a new strategy to pharmacologically interfering with ErbB receptor activity. © 2005 Wiley-Liss, Inc.
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