| 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. |
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| 3. |
- Berglund, Anders, et al.
(författare)
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ProVal : A protein-scoring function for the selection of native and near-native folds
- 2004
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Ingår i: Proteins. - : Wiley-Liss, Inc. - 0887-3585 .- 1097-0134. ; 54:2, s. 289-302
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Tidskriftsartikel (refereegranskat)abstract
- A low-resolution scoring function for the selection of native and near-native structures from a set of predicted structures for a given protein sequence has been developed. The scoring function, ProVal (Protein Validate), used several variables that describe an aspect of protein structure for which the proximity to the native structure can be assessed quantitatively. Among the parameters included are a packing estimate, surface areas, and the contact order. A partial least squares for latent variables (PLS) model was built for each candidate set of the 28 decoy sets of structures generated for 22 different proteins using the described parameters as independent variables. The C(alpha) RMS of the candidate structures versus the experimental structure was used as the dependent variable. The final generalized scoring function was an average of all models derived, ensuring that the function was not optimized for specific fold classes or method of structure generation of the candidate folds. The results show that the crystal structure was scored best in 64% of the 28 test sets and was clearly separated from the decoys in many examples. In all the other cases in which the crystal structure did not rank first, it ranked within the top 10%. Thus, although ProVal could not distinguish between predicted structures that were similar overall in fold quality due to its inherently low resolution, it can clearly be used as a primary filter to eliminate approximately 90% of fold candidates generated by current prediction methods from all-atom modeling and further evaluation. The correlation between the predicted and actual C(alpha) RMS values varies considerably between the candidate fold sets.
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| 4. |
- Bredenberg, Johan, et al.
(författare)
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Conformational states of the glucocorticoid receptor DNA-binding domain from molecular dynamics simulations
- 2002
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 49:1, s. 24-36
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics simulations (MD) have been performed on variant crystal and NMR-derived structures of the glucocorticoid receptor DNA-binding domain (GR DBD). A loop region five residues long, the so-called D-box, exhibits significant flexibility, and transient perturbations of the tetrahedral geometry of two structurally important Cys4 zinc finger are seen, coupled to conformational changes in the D-box. In some cases, one of the Cys ligands to zinc exchanges with water, although no global distortion of the protein structure is observed. Thus, from MD simulation, dynamics of the D-box could partly be explained by solvent effects in conjunction with structural reformation of the zinc finger.
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| 5. |
- Eklund, M., et al.
(författare)
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Anti-idiotypic protein domains selected from protein A-based affibody libraries
- 2002
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 48:3, s. 454-462
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Tidskriftsartikel (refereegranskat)abstract
- Three pairs of small protein domains showing binding behavior in analogy with anti-idiotypic antibodies have been selected using phage display technology. From an affibody protein library constructed by combinatorial variegation of the Fe binding surface of the 58 residue staphylococcal protein A (SPA)-derived domain Z, affibody variants have been selected to the parental SPA scaffold and to two earlier identified SPA-derived affibodies. One selected affibody (Z(SPA-1)) was shown to recognize each of the five domains of wild-type SPA with dissociation constants (K.) in the micromolar range. The binding of the Z(SPA-1) affibody to its parental structure was shown to involve the Fc binding site of SPA, while the Fab-binding site was not involved. Similarly, affibodies showing anti-idiotypic binding characteristics were also obtained when affibodies previously selected for binding to Taq DNA polymerase and human IgA, respectively, were used as targets for selections. The potential applications for these types of affinity pairs were exemplified by one-step protein recovery using affinity chromatography employing the specific interactions between the respective protein pair members. These experiments included the purification of the Z(SPA-1) affibody from a total Escherichia coli cell lysate using protein A-Sepharose, suggesting that this protein A/antiprotein A affinity pair could provide a basis for novel affinity gene fusion systems. The use of this type of small, robust, and easily expressed anti-idiotypic affibody pair for affinity technology applications, including self-assembled protein networks, is discussed.
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| 6. |
- Gutmanas, Aleksandras, et al.
(författare)
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Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes.
- 2004
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Ingår i: Proteins. - : Wiley. - 1097-0134. ; 57:4, s. 772-82
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Tidskriftsartikel (refereegranskat)abstract
- Four molecular dynamics simulation trajectories of complexes between the wild-type or a mutant Antennapedia homeodomain and 2 DNA sequences were generated in order to probe the mechanisms governing the specificity of DNA recognition. The starting point was published affinity measurements showing that a single protein mutation combined with a replacement of 2 base pairs yields a new high-affinity complex, whereas the other combinations, with changes on only 1 macromolecule, exhibited lower affinity. The simulations of the 4 complexes yielded fluctuating networks of interaction. On average, these networks differ significantly, explaining the switch of affinity caused by the alterations in the macromolecules. The network of mostly hydrogen-bonding interactions involving several water molecules, which was suggested both by X-ray and NMR structures of the wild-type homeodomain and its DNA operator sequence, could be reproduced in the trajectory. More interestingly, the high-affinity complex with alterations in both the protein and the DNA yielded again a dynamic but very tight network of intermolecular interactions, however, attributing a significantly stronger role to direct hydrophobic interactions at the expense of water bridges. The other 2 homeodomain-DNA complexes, with only 1 molecule altered, show on average over the trajectories a clearly reduced number of protein-DNA interactions. The observations from these simulations suggest specific experiments and thus close the circle formed by biochemical, structural, and computational studies. The shift from a water-dominated to a more "dry" interface may prove important in the design of proteins binding DNA in a specific manner.
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| 7. |
- Julenius, Karin, et al.
(författare)
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Coupling of ligand binding and dimerization of helix-loop-helix peptides: Spectroscopic and sedimentation analyses of calbindin D-9k EF-hands
- 2002
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 47:3, s. 323-333
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Tidskriftsartikel (refereegranskat)abstract
- Isolated Ca2+-binding EF-hand peptides have a tendency to dimerize. This study is an attempt to account for the coupled equilibria of Ca2+-binding and peptide association for two EF-hands with strikingly different loop sequence and net charge. We have studied each of the two separate EF-hand fragments from calbindin D-9k. A series of Ca2+-titrations at different peptide concentrations were monitored by CD and fluorescence spectroscopy. All data were fitted simultaneously to both a complete model of all possible equilibrium intermediates and a reduced model not including dimerization in the absence of Ca2+. Analytical ultracentrifugation shows that the peptides may occur as monomers or dimers depending on the solution conditions. Our results show strikingly different behavior for the two EF-hands. The fragment containing the N-terminal EF-hand shows a strong tendency to dimerize in the Ca2+-bound state. The average Ca2+-affinity is 3.5 orders of magnitude lower than for the intact protein. We observe a large apparent cooperativity of Ca2+ binding for the overall process from Ca2+-free monomer to fully loaded dimer, showing that a Ca2+-free EF-hand folds upon dimerization to a Ca2+-bound EF-hand, thereby presenting a preformed binding site to the second Ca2+-ion. The C-terminal EF-hand shows a much smaller tendency to dimerize, which may be related to its larger net negative charge. In spite of the differences in dimerization behavior, the Ca2+ affinities of both EF-hand fragments are similar and in the range IgK = 4.6-5.3.
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| 8. |
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| 9. |
- Linhult, M., et al.
(författare)
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Improving the tolerance of a protein a analogue to repeated alkaline exposures using a bypass mutagenesis approach
- 2004
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Ingår i: Proteins. - : Wiley. - 0887-3585 .- 1097-0134. ; 55:2, s. 407-416
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Tidskriftsartikel (refereegranskat)abstract
- Staphylococcal protein A (SPA) is a cell surface protein expressed by Staphylococcus aureus. It consists of five repetitive domains. The five SPA-domains show individual interaction to the Fc-fragment as well as certain Fab-fragments of immunoglobulin G (IgG) from most mammalian species. Due to the high affinity and selectivity of SPA, it has a widespread use as an affinity ligand for capture and purification of antibodies. One of the problems with proteinaceous affinity ligands in large-scale purification is their sensitivity to alkaline conditions. SPA however, is considered relatively stable to alkaline treatment. Nevertheless, it is desirable to further improve the stability in order to enable an SPA-based affinity medium to withstand even longer exposure to the harsh conditions associated with cleaning-in-place (CIP) procedures. For this purpose, a protein engineering strategy, which was used earlier for stabilization and consists of replacing the asparagine residues, is employed. Since Z in its nonengineered form already has a significant tolerance to alkaline treatment, small changes in stability due to the mutations are difficult to assess. Hence, in order to enable detection of improvements regarding the alkaline resistance of the Z domain, we chose to use a bypass mutagenesis strategy using a mutated variant Z(F30A) as a surrogate framework. Z(F30A) has earlier been shown to possess an affinity to IgG that is similar to the wild-type but also demonstrates decreased structural stability. Since the contribution of the different asparagine residues to the deactivation rate of a ligand is dependent on the environment and also the structural flexibility of the particular region, it is important to consider all sensitive amino acids one by one. The parental Z-domain contains eight asparagine residues, each with a different impact on the alkaline stability of the domain. By exchanging asparagine 23 for a threonine, we were able to increase the stability of the Z(F30A) domain in alkaline conditions. Also, when grafting the N23T mutation to the Z scaffold, we were able to detect an increased tolerance to alkaline treatment compared to the native Z molecule.
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| 10. |
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| 11. |
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| 12. |
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| 13. |
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| 14. |
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| 15. |
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| 16. |
- Favrin, Giorgio, et al.
(författare)
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Folding of a small helical protein using hydrogen bonds and hydrophobicity forces.
- 2002
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 47:2, s. 99-105
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Tidskriftsartikel (refereegranskat)abstract
- A reduced protein model with five to six atoms per amino acid and five amino acid types is developed and tested on a three-helix-bundle protein, a 46-amino acid fragment from staphylococcal protein A. The model does not rely on the widely used Go approximation, which ignores non-native interactions. We find that the collapse transition is considerably more abrupt for the protein A sequence than for random sequences with the same composition. The chain collapse is found to be at least as fast as helix formation. Energy minimization restricted to the thermodynamically favored topology gives a structure that has a root-mean-square deviation of 1.8 A from the native structure. The sequence-dependent part of our potential is pairwise additive. Our calculations suggest that fine-tuning this potential by parameter optimization is of limited use.
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| 17. |
- Favrin, Giorgio, et al.
(författare)
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Sequence-based study of two related proteins with different folding behaviors
- 2004
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 54:1, s. 8-12
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Tidskriftsartikel (refereegranskat)abstract
- Z(SPA-1) is an engineered protein that binds to its parent, the three-helix-bundle Z domain of staphylococcal protein A. Uncomplexed Z(SPA-1) shows a reduced helix content and a melting behavior that is less cooperative, compared with the wild-type Z domain. Here we show that the difference in folding behavior between these two sequences can be partly understood in terms of an off-lattice model with 5-6 atoms per amino acid and a minimalistic potential, in which folding is driven by backbone hydrogen bonding and effective hydrophobic attraction. (C) 2003 Wiley-Liss, Inc.
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| 18. |
- Irbäck, Anders, et al.
(författare)
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Folding thermodynamics of three beta-sheet peptides: A model study
- 2004
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 56:1, s. 110-116
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Tidskriftsartikel (refereegranskat)abstract
- We study the folding thermodynamics of a beta-hairpin and two three-stranded beta-sheet peptides using a simplified sequence-based all-atom model, in which folding is driven mainly by backbone hydrogen bonding and effective hydrophobic attraction. The native populations obtained for these three sequences are in good. agreement with experimental data. We also show that the apparent native population depends on which observable is studied; the hydrophobicity energy and the number of native hydrogen bonds give different results. The magnitude of this dependence matches well with the results obtained in two different experiments on the beta-hairpin. (C) 2004 Wiley-Liss, Inc.
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| 19. |
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| 20. |
- Novotny, Marian, et al.
(författare)
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Evaluation of protein fold comparison servers.
- 2004
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Ingår i: Proteins. - 1097-0134. ; 54:2, s. 260-70
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Tidskriftsartikel (refereegranskat)abstract
- When a new protein structure has been determined, comparison with the database of known structures enables classification of its fold as new or belonging to a known class of proteins. This in turn may provide clues about the function of the protein. A large number of fold comparison programs have been developed, but they have never been subjected to a comprehensive and critical comparative analysis. Here we describe an evaluation of 11 publicly available, Web-based servers for automatic fold comparison. Both their functionality (e.g., user interface, presentation, and annotation of results) and their performance (i.e., how well established structural similarities are recognized) were assessed. The servers were subjected to a battery of performance tests covering a broad spectrum of folds as well as special cases, such as multidomain proteins, Calpha-only models, new folds, and NMR-based models. The CATH structural classification system was used as a reference. These tests revealed the strong and weak sides of each server. On the whole, CE, DALI, MATRAS, and VAST showed the best performance, but none of the servers achieved a 100% success rate. Where no structurally similar proteins are found by any individual server, it is recommended to try one or two other servers before any conclusions concerning the novelty of a fold are put on paper.
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| 21. |
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| 22. |
- Permyakov, Eugene A, et al.
(författare)
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Ultraviolet illumination-induced reduction of alpha-lactalbumin disulfide bridges
- 2003
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Ingår i: Proteins: Structure, Function, and Bioinformatics. - : Wiley. - 0887-3585. ; 51:4, s. 498-503
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Tidskriftsartikel (refereegranskat)abstract
- Prolonged exposure of Ca2+-loaded or Ca2+-depleted human -lactalbumin to ultraviolet light (270-290 nm, 1 mW/cm2, for 2 to 4 h) results in a 10-nm red shift of its tryptophan fluorescence spectrum. Gel chromatography of the UV-illuminated samples reveals two non-native protein forms: (1) a component with a red-shifted tryptophan fluorescence spectrum; and (2) a component with kynurenine-like fluorescent properties. The first component has from 0.6 to 0.9 free DTNB-reactive SH groups per protein molecule, which are absent in the native protein and is characterized by slightly lowered Ca2+-affinity (2 × 108 M-1 versus 8 × 108 M-1 for the native protein) and absence of observable thermal transition. The second component corresponds to the protein with photochemically modified tryptophan residues. It is assumed that the UV excitation of tryptophan residue(s) in -lactalbumin is followed by a transfer of electrons to the SS bonds, resulting in their reduction. Mass spectrometry data obtained for trypsin-fragmented UV-illuminated -lactalbumin with acrylodan-modified free thiol groups reveal the reduction of the 61-77 and 73-91 disulfide bridges. The effect observed has to be taken into account in any UV-region spectral studies of -lactalbumin. Proteins 2003;51:498-503.
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| 23. |
- Villoutreix, Bruno O., et al.
(författare)
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Three-dimensional model of the SHBG-like region of anticoagulant protein S: New structure-function insights
- 2001
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Ingår i: Proteins. - 0887-3585. ; 43:2, s. 203-216
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Tidskriftsartikel (refereegranskat)abstract
- Protein S (PS) is a vitamin K-dependent glycoprotein that consists of several modules including a C-terminal sex hormone-binding globulin (SHBG)-like domain that has been subdivided into two laminin LG-type domains, The SHBG-like region of PS is known to bind to a complement regulator molecule, C4b-binding protein (C4BP), coagulation factor Va (FVa) and receptor tyrosine kinases. Inherited PS deficiency has been associated with thromboembolic disease, Yet, study of the mechanisms by which the SI-IBG-like region of PS serves its essential functions has so far been hampered because of the lack of structural information. Recently, the three-dimensional (3D) structure of LG domains from plasma SHBG, laminin and neurexin have been reported and were found related to the pentraxin family, We used these X-ray structures to build homology models of the SHBG like region of human PS, We then analyzed previously reported experimental/clinical data in the light of the predicted structures. A potential calcium-binding site is found in the first LG domain of PS and D292 could play a role in this process, This region is close to the interface between the two LG domains and is also surrounded by segments that have been suggested by synthetic peptide studies to be important for C4BP or FVa binding. The 39 point mutations linked to PS deficiencies or reported as neutral variants were rationalized in the 3D structure.
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| 24. |
- Wallin, Stefan, et al.
(författare)
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Testing similarity measures with continuous and discrete protein models
- 2003
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 50:1, s. 144-157
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Tidskriftsartikel (refereegranskat)abstract
- There are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root-mean-square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three-helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted structures are found to depend strongly on the distance measure used and the scale considered. We find that the cRMSD measure very effectively describes long-range features but is less effective with short-range features, and it correlates weakly with energy. A stronger correlation with energy and a better description of short-range properties is obtained, when we use measures based on intramolecular distances.
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| 25. |
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| 26. |
- Xue, Wei-Feng, et al.
(författare)
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Multi-method global analysis of thermodynamics and kinetics in reconstitution of monellin
- 2004
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Ingår i: Proteins. - : Wiley. - 0887-3585. ; 57:3, s. 586-595
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Tidskriftsartikel (refereegranskat)abstract
- Accurate and precise determinations of thermodynamic parameters of binding are important steps toward understanding many biological mechanisms. Here, a multi-method approach to binding analysis is applied and a detailed error analysis is introduced. Using this approach, the binding thermodynamics and kinetics of the reconstitution of the protein monellin have been quantitatively determined in detail by simultaneous analysis of data collected with fluorescence spectroscopy, surface plasmon resonance and isothermal titration calorimetry at 25degreesC, pH 7.0 and 150 mM NaCl. Monellin is an intensely sweet protein composed of two peptide chains that form a single globular domain. The kinetics of the reconstitution reaction are slow, with an association rate constant, k(on) of 8.8 x 10(3) M-1 s(-1) and a dissociation rate constant, k(off) of 3.1 x 10(-4) s(-1). The equilibrium constant K-A is 2.8 x 10(7) M-1 corresponding to a standard free energy of association, DeltaGdegrees, of -42.5 kJ/mol. The enthalpic component, DeltaHdegrees, is -18.7 kJ/moI and the entropic contribution, DeltaSdegrees, is 79.8 J mol(-1) K-1 (-TDeltaSdegrees = -23.8 kJ/mol). The association of monellin is therefore a bimolecular intra-protein association whose energetics are slightly dominated by entropic factors. (C) 2004 Wiley-Liss, Inc.
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