摘要:

AbstractThe DNA‐binding helix pairs in gene repressor and activator were compared with other approximately perpendicular pairs of adjacent helices in the known protein structures. Two other examples of closely matching conformations were found in cytochromecperoxidase (residues 153–174) and in ribosomal L7/L12 protein (residues 68–89). Another group of such offset “lap‐joints” are the Ca‐binding “EF hand” structures, which bind a positive rather than a negative ligand. The EF hands turn out to match the DNA‐binding motifs quite well (outside of the loop) if their sequence direction is reversed. This conformation is thus not as unusual as had been thought, but may have a more generalized role in ion binding and occasionally occur in a pur

ISSN:0887-3585    

DOI:10.1002/prot.340040402

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

年代:1988

数据来源: WILEY

摘要:

AbstractTwo new globin structures have recently been determined at high resolution: the globin from the molluscAplysia limacinaat 1.6 A resolution and a new refinement of the structure from sea lamprey. Two amino acid sequences of these homologous molecules have only 30% residue identity in an optimal alignment. We discuss some of the problems arising in the alignment ofAplysiaglobin with other globins of known structure, a challenging problem because of the distant relationship. Four independent approaches were applied to the alignment of theAplysiaand lamprey globins, including those based on individual sequence comparisons, structural analysis, and the relatively new method of templates or fingerprints derived for an entire family of proteins. We also compare these two new structures with what is already known about the globin family. A detailed description of the two structures shows that the two molecules contain the main structural features common to all the globins so far studied with several minor but interesting hitherto unobserved variations.

ISSN:0887-3585    

DOI:10.1002/prot.340040403

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

年代:1988

数据来源: WILEY

摘要:

AbstractTwo very different mechanisms of folding have been proposed from experimental studies of disulfide formation in reduced ribonuclease A. (1) A pathway in which the rate‐limiting step separates fully folded protein from all other disulfide intermediates and occurs solely in three‐disulfide intermediates. (2) A multiple pathway mechanism with different rate‐limiting steps for each pathway. The various rate‐limiting steps involve disulfide breakage, formation, and rearrangement in intermediates with one, two, three, and four protein disulfides. To distinguish between these two mechanisms, we have carried out further studies of both unfolding and refolding.Refolding of reduced ribonuclease A requires three‐disulfide intermediates to accumulate; negligible refolding occurs when only the nearly random one‐ and two‐disulfide intermediate species are populated. Therefore, no rate‐limiting steps of the type postulated in mechanism (2) occur in intermediates with one and two protein disulfides. Unfolding and disulfide reduction is an all‐or‐none process; no disulfide intermediates accumulate to detectable to detectable levels or precede the rate‐limiting step. Mechanism (2) requires that such intermediates precede the rate‐limiting step and accumulate to substantial levels.The different proposal were shown not to result from the use of different solution conditions or disulfide reagents; the two sets of data are not inconsistent. Instead, the inappropriate mechanism (2) resulted from an incorrect kinetic analysis and misinterpretation of the kinetics of disulfide

ISSN:0887-3585    

DOI:10.1002/prot.340040404

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

年代:1988

数据来源: WILEY

摘要:

AbstractMethods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high‐resolution crystal structure. In addition, a two‐step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin.The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945 Å resolution (Hendrickson, W.A., Teeter, M.M.Nature290:107–113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S. W., Glöckner,J. Biochemistry20:33–37, 1981) as modified (Manavalan, P., Johnson, W. C., Jr.Anal. Biochem.167:76–85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane‐active toxins homologous to crambin (α1‐ and β‐purothionin, phoratoxin A and B, an viscotoxin A3 and B).The new program SEQ (pronounced “seek”) was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location.Both CD‐arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of Purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD

ISSN:0887-3585    

DOI:10.1002/prot.340040405

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

年代:1988

数据来源: WILEY

摘要:

AbstractThe structure of human erythrocytic carbonic anhydrase II has been refined by constrained and restrained structure–factor least‐squares refinement at 2.0 Å resolution. The conventional crystallographic R value is 17.3%. Of 167 solvent molecules associated with the protein, four are buried and stabilize secondary structure elements. The zinc ion is ligated to three histidyl residues and one water molecule in a nearly tetrahedral geometry. In addition to the zinc‐bound water, seven more water molecules are identified in the active site. Assuming that Glu‐106 is deprotonated at pH 8.5, some of the hydrogen bond donor–acceptor relations in the active site can be assigned and are described here in detail. The Oγ1 atom of Thr‐199 donates its proton to the Oε1 atom of Glu‐106 and can function as a hydrogen bond acceptor only in additiona

ISSN:0887-3585    

DOI:10.1002/prot.340040406

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

年代:1988

数据来源: WILEY

摘要:

AbstractThe binding of four inhibitors—mercuric ion, 3‐acetoxymercuri‐4‐aminobenzenesulfonamide (AMS), acetazolamide (Diamox), and thiocyanate ion—to human carbonic anhydrase II (HCA II) has been studied with X‐ray crystallography.The binding of mercury to HCA II at pH 7.0 has been investigated at 3.1 Å resolution. Mercuric ions are observed at both nitrogens in the His‐64 ring. One of these sites is pointing toward the zinc ion. The only other binding site for mercury is at Cys‐206.The binding of the two sulfonamide inhibitors AMS and Diamox, has been reinvestigated at 2.0 and 3.0 Å, respectively. Only the nitrogen of the sulfonamide group binds to the zinc ion replacing the hydroxyl ion. The sulfonamide oxygen closet to the zinc ion is 3.1 Å away. Thus the tetrahedral geometry of the zinc is retained, refuting earlier models of a pentacoordinated zinc.The structure of the thiocyanate complex has been investigated at pH 8.5 and the structure has been refined at 1.9 Å resolution using the least‐squares refinement program PROLSQ. The crystallographicRfactor is 17.6%. The zinc ion is pentacoordinated with the anion as well as a water molecule bound in addition to the three histidine residues. The nitrogen atom of the SCN−ion is 1.9 Å from the zinc ion but shifted 1.3 Å with respect to the hydroxyl ion in the native structure and at van der Waals' distance from the Oγl atom of Thr‐199. This is due to the inability of the Oγl atom of Thr‐199 to serve as a hydrogen bond donor, thus repelling the nonprotonated nitrogen. The SCN−molecule reaches into the deep end of the active site cavity where the sulfur atom has displaced the so‐called “deep” water molecule of the native enzyme. The zinc‐bound water molecule is 2.2 Å from the zinc ion and 2.4 Å from the SCN−nitrogen. In addition, this water is hydrogen bonded to the Oγl atom of Thr‐199 and to another water molecule.We have observed that solvent and inhibitor molecules have three possible binding sites on the zinc ion and their significance for the catalysis and inhibition of HCA II will be discussed. All available crystallographic data are consistent with a proposed catalytic mechanism in which both the OH moiety and one oxygen of th

ISSN:0887-3585    

DOI:10.1002/prot.340040407

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

年代:1988

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340040408

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

年代:1988

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340040401

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

年代:1988

数据来源: WILEY