ISSN:0887-3585    

DOI:10.1002/prot.340080202

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

年代:1990

数据来源: WILEY

摘要:

Abstractα1‐Purothionin (α1‐P), a wheatgerm protein and lytic toxin, has a secondary and tertiary structure similar to that of crambin as revealed by CD and NMR studies. α1‐P crystallizes in the tetragonal space group I422 with unit cell dimensions:a=b= 53.59 andc= 69.79 Å. X‐ray diffraction data have been measured to 2.5 Å Bragg spacing. The crystal structure has been determined by molecular replacement methods, using an energy‐minimized α1‐P model structure derived from crambin (Whitlow and Teeter:Journal of Biomolecular Structure and Dynamics2:831–848, 1985,Journal of the American Chemical Society108:7163–7172, 1986). The energy‐minimized model gives a slightly cleaner rotation solution and better refinement against the x‐ray data than do the crambin or unminimized α1‐P structures. The final crystallographic residual with the data in the 10–2.5 Å resolution range is 0.216. The refined α1‐P structure has a backbone rms difference of 0.74 Å from crambin and 0.55 Å from the energy‐minimized α1‐P model. A low resolution NMR model of α1‐P calculated from metric matrix distance geometry and restrained molecular dynamics differs from crambin's backbone by 2.3 Å rms deviation (Clore et al.:EMBO Journal5:2729–2735, 1986). Backbone dihedral angles for our predicted model differ from the refined α1‐P structure in only one region (at a turn where there is a deletion relative to cramb

ISSN:0887-3585    

DOI:10.1002/prot.340080203

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

年代:1990

数据来源: WILEY

摘要:

AbstractGlobins and phycocyanins are two classes of proteins with different function, different ligands, and no substantial sequence similarity, yet the conformations of their polypeptide chains show very similar folding patterns. Does this arise from a genuine, albeit very distant, evolutionary relationship, or does it represent a common solution of a structural problem? We address this question by a very detailed comparison of the structures of the two protein families. An analysis of the helices and their interactions shows many features common to globins and phycocyanins, including some exceptional features of the globins such as a 3–10Chelix and the unusual “crossed‐ridge” packing pattern at theB/Ehelix interfaces. We conclude that the evidence supports the hypothesis of distant evolutionary relationship between globins and phyco

ISSN:0887-3585    

DOI:10.1002/prot.340080204

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

年代:1990

数据来源: WILEY

摘要:

AbstractA common sequence/structural motif pattern has been identified within the steroid/thyroid hormone receptors and other transcriptional activators using a new massively parallel symbolic learning assistant computer system. The pattern appears nearly diagnostic of transcription activation, including relative activation strength, among nuclear and DNA‐binding prokaryotic proteins. In cases where mutation/deletion/chimeric studies have identified the activation domain, the pattern matches within that domain. These facts and the nature of the pattern itself strongly support the idea that the patterned domain is directly involved in a protein‐protein transcription activation interact

ISSN:0887-3585    

DOI:10.1002/prot.340080205

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

年代:1990

数据来源: WILEY

摘要:

AbstractThree scorpion toxins have been analyzed by circular dichroism in water and in 2,2,2‐trifluoroethanol (TFE) solutions. These toxins were chosen because they are representative of three kinds of pharmacological activities: (1) toxin AaH IT2, an antiinsect toxin purified from the venom ofAndroctonus australis Hector, which is able to bind to insect nervous system preparation, (2) toxin Css II, from the venom ofCentruroides suffusus suffusus, which is a β‐type antimammal toxin capable of binding to mammal nervous system preparation, and (3) the toxin Ts VII from the venom ofTityus serrulatus, which is able to bind to both types of nervous systems. In order to minimize bias, CD data were analyzed by a predictive algorithm to assess secondary structure content. Among the three molecules, Ts VII presented the most unordered secondary structure in water, but it gained in ordered forms when solubilized in TFE. These results indicated that the Ts VII backbone is the most flexible, which might result in a more pronounced tendency for this toxin molecule to undergo conformational changes. This is consistent with the fact that it competes with both antiinsect and β‐type antimammal toxins for the binding to the sodium

ISSN:0887-3585    

DOI:10.1002/prot.340080206

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

年代:1990

数据来源: WILEY

摘要:

AbstractA compact mitochondrial gene contains all essential information about the synthesis of mitochondrial proteins which play their roles in a small compartment of the mitochondrium. Almost no noncoding regions have been found through the gene, but a necessary set of tRNAs for the 20 amino acids is provided for biosynthesis, some of them coding different amino acids from those in a usual cell. Since the gene is so compact that the produced proteins would have some characteristic aspects for the mitrochondrium, amino acid compositions of mitochondrial proteins (mt‐proteins) were examined in the 20‐dimensional composition space. The results show that compositions of proteins translated from the mitochondrial genes have a distinct character having more hydrophobic content than others, which is illustrated by a clustered distribution in the multidimensional composition space. The cluster is located at the tail edge of the global distribution pattern of a Gaussian shape for other various kinds of proteins in the space. The mt‐proteins are rich in hydrophobic amino acids as is a membrane protein, but are different from other membrane proteins in a lesser content of Val. A good correlation found between the base and amino acid compositions for the mitochondria was examined in comparison to those of organisms such as thermophilic bacterium having an extreme G‐C‐rich base co

ISSN:0887-3585    

DOI:10.1002/prot.340080207

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

年代:1990

数据来源: WILEY

摘要:

AbstractA new procedure for the graphic analysis of molecular dynamics (MD) simulations on proteins is introduced, in which comprehensive visualization of results and pattern recognition is greatly facilitated. The method involves determining the conformational and helicoidal parameters for each structure entering the analysis via the method “Curves,” developed for proteins by Sklenar, Etchebest, and Lavery (Proteins: Structure, Function Genet. 6:46–60, 1989) followed by a novel computer graphic display of the results. The graphic display is organized systematically using conformation wheels (“dials”) for each torsional parameter and “windows” on the range values assumed by the linear and angular helicoidal parameters, and is present in a form isomorphous with the primary structure per se. The complete time evolution of dynamic structure can then be depicted in a set of four composite figures. Dynamic aspects of secondary and tertiary structure are also provided. The procedure is illustrated with an analysis of a 50 psec in vacuo simulation on the 58 residue protein, bovine pancreatic trypsin inhibitor (BPTI), in the vicinity of the local minimum on the energy surface corresponding to a high resolution crystal structure. The time evolution of 272 conformational and 788 helicoidal parameters for BPTI is analyzed. A number of interesting features can be discerned in the analysis, including the dynamic range of conformational and helicoidal motions, the dynamic extent of 2° structure motifs, and the calculated fluctuations in the helix axis. This approach is expected to be useful for a critical analysis of the effects of various assumptions about force field parameters, truncation of potentials, solvation, and electrostatic effects, and can thus contribute to the development of more reliable simulation protocols for proteins. Extensions of the analysis to present differential changes in conformational and helicoidal parameters is expected to be valuable in MD studies of protein complexes with substrates, inhibitors, and effectors and in determining the nature of structural changes in protein–prot

ISSN:0887-3585    

DOI:10.1002/prot.340080208

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

年代:1990

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340080201

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

年代:1990

数据来源: WILEY