Structure of bovine pancreatic trypsin inhibitor

Wlodawer, Alexander; Walter, J.; Huber, Robert; Sjölin, L.

doi:10.1016/s0022-2836(84)80006-6

Cited by 464 publications

(287 citation statements)

References 43 publications

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“…Experimental results for BPTI in panel a refer to the free energy changes evaluated from the exchange rates observed at 30°C and pH 3.5 (19). The coordinates of the BPTI R-carbons for GNM calculations are taken from the neutron and X-ray refined structure of BPTI (33). In panel b the bars indicate the data from the HX experiments on cyt c (11), and the solid curve represents the results from GNM calculations using the crystal structure of horse heart cyt c at low ionic strength (37).…”

Section: Results and Comparison With Hx Experimentsmentioning

confidence: 99%

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

et al. 1998

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Recently, we developed a simple analytical model based on local residue packing densities and the distribution of tertiary contacts for describing the conformational fluctuations of proteins in their folded state. This so-called Gaussian network model (GNM) is applied here to the interpretation of experimental hydrogen exchange (HX) behavior of proteins in their native state or under weakly denaturing conditions. Calculations are performed for five proteins: bovine pancreatic trypsin inhibitor, cytochrome c, plastocyanin, staphylococcal nuclease, and ribonuclease H. The results are significant in two respects. First, a good agreement is reached between calculated fluctuations and experimental measurements of HX despite the simplicity of the model and within computational times 2 or 3 orders of magnitude faster than earlier, more complex simulations. Second, the success of a theory, based on the coupled conformational fluctuations of residues near the native state, to satisfactorily describe the native-state HX behavior indicates the significant contribution of local, but cooperative, fluctuations to protein conformational dynamics. The correlation between the HX data and the unfolding kinetics of individual residues further suggests that local conformational susceptibilities as revealed by the GNM approach may have implications relevant to the global dynamics of proteins.Hydrogen exchange (HX) data for proteins directly indicate the relative accessibility of various protons to solvent, typically under conditions that can be denaturing to different extents. Observed HX times can vary over extremely broad ranges, from instantaneous to months. Generally these various times have been interpreted and ascribed to several kinds of processesslocal fluctuations for the fastest, local unfolding for intermediate, and global unfolding for the slowest exchanges (1). Some disagreements have arisen between the descriptions of the underlying kinetic processes and the interpretation of HX mechanisms because of differences in the operational definitions of these processes (2). HX from native proteins was recently pointed out to monitor with a remarkable precision rapid conformational fluctuations of the order of microseconds to milliseconds, while no correlation could be observed between HX free energies of individual residues and their unfolding rates which are several orders of magnitude slower than local fluctuations (3). Global unfolding rates are expected to be the same for all residues, while the superimposed exchange rates due to residue fluctuations vary depending on local interactions (4, 1, 5). Here we will avoid ascribing rates to specific processes but instead investigate directly the extent of protection in the native state and compare this with the measured exchange rates. This analysis has become possible with the development of a new simple model of protein structure and dynamics, recently proposed for analyzing the conformational fluctuations of folded proteins (6, 7).Two limits, or two mechanisms of ex...

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Section: Results and Comparison With Hx Experimentsmentioning

confidence: 99%

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

et al. 1998

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“…The crystal forms of F22A, Y23A, and F45A are isomorphous and are also closely related to the native form I1 (Wlodawer et al, 1984). However, there is a 7% reduction in the length of the unit cell a-axis in the crystals of the mutant proteins as compared to the native form 11.…”

Section: Crystal Structure Refinement and Model Buildingmentioning

confidence: 95%

“…Comparisons are drawn between each mutant and the wild-type crystal structure of the same space group, in order to minimize any differences that might be related to crystal packing. Therefore N43G is compared to 6PT14 (form 111) (Wlodawer et al, 1987b) and the other three mutants are compared to 5PT14 (form 11) (Wlodawer et al, 1984).…”

Section: Comparison Of Atomic Positions Of Mutants With Wild-typementioning

confidence: 99%

Crevice‐forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: Crystal structures of F22A, Y23A, N43G, and F45A

et al. 1993

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Crystal structures of four mutants of bovine pancreatic trypsin inhibitor (F22A, Y23A, N43G, and F45A), engineered to alter their stability properties, have been determined. The mutated residues, which are highly conserved among Kunitz-type inhibitors, are located in the rigid core of the molecule. Replacement of the partially buried bulky residues of the wild-type protein with smaller residues resulted in crevices open to the exterior of the molecule. The overall three-dimensional structure of these mutants is very similar to that of the wild-type protein and only small rearrangements are observed among the atoms lining the crevices.

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“…Bovine ribonuclease is one of the best studied proteins by X-ray diffraction on single crystals (for a review see Wlodawer, 1985). It was the third enzyme whose crystal structure was solved.…”

Section: Ribonucleasementioning

confidence: 99%

Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals

Billeter¹

1992

Quart. Rev. Biophys.

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Following the first determinations of protein structures in the late 1950s and the early 1960s (see for example Kendrewet al.1960; Perutz, 1964), the three-dimensional structures of several hundred proteins have been elucidated by X-ray diffraction on single crystals. By the end of 1991, approximately 150 entries of proteins with substantially different sequences and a well resolved structure (Hobohmet al.1992) were deposited in the Protein Data Bank (Bernsteinet al.1977; Abolaet al.1987). In addition, many structures of homologous proteins or of mutants have been described, bringing the total number of entries to about 600. While it was soon accepted that almost all of these structures do indeed give a correct picture of the fold of the active protein in spite of the non-physiological environment of single crystals, it is not clear to what extent structural details are reliably described by these structures. In particular the surface of a protein may be modified due to the dense packing of protein molecules in the crystal lattice. A detailed knowledge of the protein surface is, however, essential for the understanding of the function of the protein.

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Structure of bovine pancreatic trypsin inhibitor

Cited by 464 publications

References 43 publications

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

Correlation between Native-State Hydrogen Exchange and Cooperative Residue Fluctuations from a Simple Model

Crevice‐forming mutants in the rigid core of bovine pancreatic trypsin inhibitor: Crystal structures of F22A, Y23A, N43G, and F45A

Comparison of protein structures determined by NMR in solution and by X-ray diffraction in single crystals

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