摘要:

AbstractCalcium‐free calmodulin‐(CaM) is rapidly hydrolyzed by proteases from both human immunodeficiency viruses (HIV) 1 and 2. Kinetic analysis reveals a sequential order of cleavage by both proteases which initiates in regions of the molecule known from X‐ray crystallographic analysis of Ca2+/CaM to be associated with calcium binding. Although HIV‐1 and HIV‐2 proteases hydrolyze two bonds in common, the initial site of cleavage required for subsequent events differs in each case. The first bond hydrolyzed by the HIV‐1 protease in the Asn‐Tyr linkage in the sequence,‐N‐I‐D‐G‐D‐G‐Q‐V‐N‐Y‐E‐E, found in the fourth calcium binding loop. In contrast, it is an Ala‐Ala bond in the third calcium loop, ‐D‐K‐D‐G‐N‐G‐Y‐I‐S‐A‐A‐E‐, that is first hydrolyzed by the HIV‐2 enzyme, followed in short order by cleavage of the same Asn‐Tyr linkage described above. Thereafter, both enzymes proceed to hydrolyze additional peptide bonds, some in common, some not. Considerable evidence exists that inhibitors are bound to the protease in an extended conformation and yet all of the cleavages we observed occur within, or at the beginning of helices in Ca2+/CaM, regions that also appear to be insufficiently exposed for protease binding. Molecular modeling studies indicate that CaM in solution must adopt a conformation in which the first cleavage site observed for each enzyme is unshielded and extended, and that subsequent cleavages involve further unwinding of helices. The conclusion that the conformation of CaM is different from that of Ca2+/CaM is supported by the observation that Ca2+/CaM is resistant to hydrolysis by either enzyme. As well as demonstrating conformational differences between CaM and Ca2+/CaM, these studies provide further evidence that the two highly homologous human retroviral proteases may be distinguished enzymologically in terms of differential substrate specificities. In addition, some new and unpredicted sequences have been identified that undergo cleavage by these enzymes. Finally, the fact that an abundant, ubiquitous, and biologically important cellular protein is broken down by the HIV proteases could be physiologically relevant to HIV infe

ISSN:0887-3585    

DOI:10.1002/prot.340100102

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractCrystals of bacteriophage T4 lysozyme used for structural studies are routinely grown from concentrated phosphate solutions. It has been found that crystals in the same space group can also be grown from solutions containing 0.05 M imidazole chloride, 0.4 M sodium choride, and 30% polyethylene glycol 3500. These crystals, in addition, can also be equilibrated with a similar mother liquor in which the sodium chloride concentration is reduced to 0.025 M. The availability of these three crystal variants has permitted the structure of T4 lysozyme to be compared at low, medium, and high ionic strength. At the same time the X‐ray structure of phage T4 lysozyme crystallized from phosphate solutions has been further refined against a new and improved X‐ray diffraction data set.The structures of T4 lysozyme in the crystals grown with polyethylene glycol as a precipitant, regardless of the sodium chloride concentration, were very similar to the structure in crystals grown from concentrated phosphate solutions. The main differences are related to the formation of mixed disulfides between cysteine residues 54 and 97 and 2‐mercaptoethanol, rather than to the differences in the salt concentration in the crystal mother liquor. Formation of the mixed disulfide at residue 54 resulted in the displacement of Arg‐52 and the disruption of the salt bridge between this residue and Glu‐62.Other than this change, no obvious alterations in existing salt bridges in T4 lysozyme were observed. Neither did the reduction in the ionic strength of the mother liquor result in the formation of new salt bridge interactions. These results are consistent with the ideas that a crystal structure determined at high salt concentrations is a good representation of the structure at lower ionic strengths, and that models of electrostatic interactions in proteins that are based on crystal structures determined at high salt concentrations are likely to be relevant at physiological ionic

ISSN:0887-3585    

DOI:10.1002/prot.340100103

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractWhen calculating three‐dimensional structures from NMR data, alternative solutions with very large RMS deviation can be obtained. Sometimes local or global inversions of the protein folding can be observed. We call these different solutions topological mirror images, as they keep the correct amino acid chirality. They are observed when the number of restraints is insufficient and represent different solutions from the same scalar information. Therefore they are common in small peptides where the NMR data are often limited and the secondary structure is not very well defined. They can also be observed in large molecules in regions of higher flexibility. In our experience the observation of topological mirror images is independent of the efficiency of sampling of the algorithm used. We present four examples of proteins with different size and folding. We also discuss ways to distinguish among the different solution

ISSN:0887-3585    

DOI:10.1002/prot.340100104

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractTriosephosphate isomerase has an important loop near the active site which can exist in a “closed” and in an “open” conformation. Here we describe the structural properties of this “flexible” loop observed in two different structures of trypanosomal triosephosphate isomerase. Trypanosomal triosephosphate isomerase, crystallized in the presence of 2.4Mammonium sulfate, packs as an asymmetric dimer of 54,000 Da in the crystallographic asymmetric unit. Due to different crystal contacts, peptide 167–180 (the flexible loop of subunit‐1) is an open conformation, whereas in subunit‐2, this peptide (residues 467–480) is in a closed conformation. In the closed conformation, a hydrogen bond exists between the tip of the loop and a well‐defined sulfate ion which is bound to the active site of subunit‐2. Such an active site sulfate is not present in subunit‐1 due to crystal contacts. When the native (2.4 M ammonium sulfate) crystals are transferred to a sulfate‐free mother liquor, the flexible loop of subunit‐2 adopts the open conformation. From a closed starting model, this open conformation was discovered through molecular dynamics refinement without manual intervention, despite involving Cα shifts of up to 7 Å. The tip of the loop, residues 472, 473, 474, and 475, moves as a rigid body. Our analysis shows that in this crystal form the flexible loop of subunit‐2 faces a solvent channel. Therefore the open and the closed conformations of this flexible loop are virtually unaffected by crystal contacts. The actual observed conformation depends only on the absence or presence of a s

ISSN:0887-3585    

DOI:10.1002/prot.340100105

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractCrystals of triosephosphate isomerase fromTrypanosoma brucei bruceihave been used in binding studies with three competitive inhibitors of the enzyme's activity. Highly refined structures have been deduced for the complexes between trypanosomal triosephosphate isomerase and a substrate analogue (glycerol‐3‐phosphate to 2.2 Å), a transition state analogue (3‐phosphonopropionic acid to 2.6 Å), and a compound structurally related to both (3‐phosphoglycerate to 2.2 Å). The active site structures of these complexes were compared with each other, and with two previously determined structures of triosephosphate isomerase either free from inhibitor or complexed with sulfate. The comparison reveals three conformations available to the “flexible loop” near the active site of triosephosphate isomerase: open (no ligand), almost closed (sulfate), and fully closed (phosphate/phosphonate complexes). Also seen to be sensitive to the nature of the active site ligand is the catalytic residue Glu‐167. The side chain of this residue occupies one of two discrete conformations in each of the structures so far observed. A “swung out” conformation unsuitable for catalysis is observed when sulfate, 3‐phosphoglycerate, or no ligand is bound, while a “swung in” conformation ideal for catalysis is observed in the complexes with glycerol‐3‐phosphate or 3‐phosphonopropionate. The water structure of the active site is different in all five structures. The results are discussed with respect to the triosephosphate isomerase structure function relationship, and with respect to an on‐going drug design project aimed at the selective inhibition

ISSN:0887-3585    

DOI:10.1002/prot.340100106

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

摘要:

AbstractThe thermally assisted diffusion of a small ligand (carbon monoxide) through a protein matrix (lupine leghemoglobin) is investigated computationally. The diffusion paths are calculated by a varient of the time‐dependent Hartree approximation which we call LES (locally enhanced sampling). The variant which was recently introduced by Elber and Karplus1is based on the classical TD‐SCF approximation of Gerber et al.2The simulation enables more significant search for diffusion pathways than was possible before. This is done by increasing the number ofligandtrajectories using a single trajectory for the protein. We compare qualitatively diffusion rates in leghemoglobin and in myoglobin. The calculation shows that the diffusion in leghemoglobin is much faster than the diffusion in myoglobin, in agreement with experiment. The gate in leghemoglobin is opened by fluctuations at a close contact between the B/C and the G helices. The most relevant fluctuation is therigidshift of the C helix with respect to the G helix. This path is not observed in a comparable calculation for myoglobin.1This finding is rationalized by the lack of the D helix in leghemoglobin and a significantly more flexible CE loop. Supporting experimental evidence for the importance of the CE loop in leghemoglobin can be found in the kinetics studies of Gibson et a

ISSN:0887-3585    

DOI:10.1002/prot.340100107

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340100101

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1991

数据来源: WILEY