摘要:

AbstractWe present a geometric analysis of the allosteric interface in the new Y state quaternary structure observed in liganded mutant hemoglobin Ypsilanti (β99 Asp → Tyr) by Smith, F.R., Lattman, E.E., Carter, C.W., Jr. (Proteins 10:81–91, 1991). The classical T to R quaternary structure change being a rotation of αβ dimers about an axis which is approximately parallel to the dimer axis of pseudosym‐metry, the new quaternary structure is obtained by applying to R an additional rotation about an axis orthogonal to the first. This suggests that Y is a modified R state rather than an intermediate on the T to R pathway. Computer docking experiments designed to simulate the quaternary structure change support this suggestion. © 1993 Wiley

ISSN:0887-3585    

DOI:10.1002/prot.340150102

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe binding free energy difference for the Gly‐169 → Ala‐169 (G169A) mutation in subtilisin BPN′ complexed with a tripeptide substrate analogue is explored using the thermodynamic integration approach. The structure of the mutant enzyme–substrate complex obtained from free energy simulation is in good agreement with experimental X‐ray refinement. The near perfect reversibility is obtained in the present work for ensuring the correctness of the free energy calculations. The results of the binding free energy difference are close to similar experimental data. © 1993 Wil

ISSN:0887-3585    

DOI:10.1002/prot.340150103

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

年代:1993

数据来源: WILEY

摘要:

AbstractA combination of dynamic Monte Carlo simulation techniques with a hydropathy scale method for the prediction of the location of transmembrane fragments in membrane proteins is described. The new hydropathy scale proposed here is based on experimental data for the interactions of tripeptides with phospholipid membranes (Jacobs, R.E., White, S.H. Biochemistry 26:6127–6134, 1987) and the self‐solvation effect in protein systems (Roseman, M.A., J. Mol. Biol. 200:513–522, 1988). The simulations give good predictions both for the state of association and the orientation of the peptide relative to the membrane surface of a number of peptides including Magainin2, M2δ, and melittin. Furthermore, for Pf1 bacterio‐phage coat protein, in accord with experiment, the simulations predict that the C‐terminus forms a transmembrane helix and the N‐terminus forms a helix which is adsorbed on the surface of the bilayer. Finally, the present series of simulations provide a number of insights into the mechanism of insertion of peptides into cell membranes. © 1993 Wi

ISSN:0887-3585    

DOI:10.1002/prot.340150104

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

年代:1993

数据来源: WILEY

摘要:

AbstractMany of the bilayer spanning segments of membrane transport proteins contain proline residues, and most of them are believed to occur in α‐helical form. A proline residue in the middle of an α‐helix is known to produce a bend in the helix, and recent studies have focused on characterizing such a bend at atomic level. In the present case, molecular dynamics (MD) studies are carried out on helix F model of bacteriorhodopsin (BR) Ace‐(Ala)7‐Trp‐(Ala)2‐Tyr‐Pro‐(Ala)2‐Trp‐(Ala)8‐NHMe and compared with Ace‐(Ala)7‐Trp‐(Ala)2‐Tyr‐(Ala)3‐Trp‐(Ala)8‐NHMe in which the proline is replaced by alanine. The bend in the helix is characterized by structural parameters such as kink angle (α), wobble angle (θ), virtual torsion angle (ρ), and the hydrogen bond distance d (Op−3… Np+1). The average values and the flexibility involved in these parameters are evaluated. The correlation among the bend related parameters are estimated. The equilibrium side chain orientations of tryptophan and tyrosine residues are discussed and compared with those found in the recently proposed model of bacteriorhodopsin. Finally, a detailed characterization of the bend in terms of secondary structures such as αI, αIIand goniometric helices are discussed, which can be useful in the interpretation of the experimental results on the secondary structures of membrane proteins invol

ISSN:0887-3585    

DOI:10.1002/prot.340150105

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

年代:1993

数据来源: WILEY

摘要:

AbstractTwo mutants of adenylate kinase fromEscherichia colihave been crystallized and analyzed by X‐ray diffraction at resolutions of 3.4 and 2.4 Å, respectively. These mutants are Pro‐9→Leu and Gly‐10→Val. They were selected for their positions in the highly conserved Gly‐loop forming a giant anion hole for the β‐phosphate of ATP (GTP) in adenylate kinases, H‐ras‐p21, and other nucleotide‐binding proteins. Mutants at these positions of H‐ras‐p21 cause cancer. In adenylate kinase these mutations cause smallish changes at the active site. Relating the structural changes to the known changes in catalysis indicates that these mutants hinder the induced‐fit movements. As a side result we find that mutant Pro‐9→Leu and wild‐type form one very similar crystal packing contact that is crystallographic in one case and noncrystallographic in the other, while all other packing contacts and the space groups are quite at

ISSN:0887-3585    

DOI:10.1002/prot.340150106

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

年代:1993

数据来源: WILEY

摘要:

AbstractWe introduce a new method for assessing the extent of residue exposure in proteins. For each atom of every residue a Gaussian‐weighted atomic surroundings value (the G‐neighborhood) is calculated. A normalized sum of G‐neighborhood values over all the atoms of a residue is complementary to conventional surface accessibility characteristics. The G‐0neighborhood value of a residue is a sensitive indicator of its location, strongly dependent on the 3D structure of a the protein. Correlations between secondary structures and patterns of G‐neighborhood values for six different protein molecules are discussed. Comparison of the distribution of hydrophobic and charged residues in the 3D structure for the alcohol‐soluble protein crambin and that of five water‐soluble proteins (cytochromec, flavodoxin, myoglobin, rhodanese, and Bence–Jones protein) shows striking differences in their G‐neighborhood patterns. Contacts between the prosthetic group and the peptide portion of a protein as well as protein interdomain contacts and monomer–monomer contacts are characterized. ©

ISSN:0887-3585    

DOI:10.1002/prot.340150107

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

年代:1993

数据来源: WILEY

摘要:

AbstractAn analysis of the tendency of hydrophobic groups to tight packing on the surface of β‐sheets based on well‐known parameters of β‐sheets and hydrophobic groups was conducted. This analysis shows the existence of very limited numbers and clearly outlined architecture families of regular parts for the majority of β‐structure‐containing domains. Each family of architecture strongly depends on the number of β‐strands in the pure β‐domains and on the existence and number of additional α‐helixes and on the mutual arrangements β‐strands and α‐helixes along the chain in mixed α/β‐domains. This paper demonstrates that the tendency of hydrophobic groups to the local tight packing on the surface of β‐sheets is probably the main reason for the twist o

ISSN:0887-3585    

DOI:10.1002/prot.340150108

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe vibrational entropy of native BPTI, with three disulfide bonds, was determined by use of normal mode calculations and compared with that of folded variants having either one less disulfide bond or lacking a peptide bond at the trypsin‐reactive site. Favorable contributions to the free energy of 2.5–5.1 kcal/mol at 300 K were calculated for the reduction of disulfide bonds in the folded state, whereas no favorable contribution was found for the hydrolysis of the peptide bond cleaved by trypsin. This is on the order of the effect of disulfides in the unfolded state. The implications of these results for the stabilization of a folded protein by the introduction of crosslinks are discussed. © 1993 Wiley‐Lis

ISSN:0887-3585    

DOI:10.1002/prot.340150109

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

年代:1993

数据来源: WILEY

摘要:

AbstractA complex of carbonic anhydrase (CA) with one of its substrates, bicarbonate, has been studied crystallographically. Human isoenzyme II was mutated at position 200 from threonine to histidine, which results in higher affinity for bicarbonate. The HCO 3−ion binds in the active site to the zinc ion as a pseudo‐bidentate ligand which gives the metal a coordination geometry between tetrahedral and trigonal bipyramide. The water/hydroxide normally bound with tetrahedral coordination to the zinc is probably replaced by the OH group of the bicarbonate ion. The importance of residues Thr‐199 and Glu‐106 in controlling the binding orientation of HCO 3−is discussed as well as the catalytic mechanism. Both the complex as well as the uncomplexed mutant were studied at 1.9 Å resolution. © 1993

ISSN:0887-3585    

DOI:10.1002/prot.340150110

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

年代:1993

数据来源: WILEY

摘要:

Abstractα‐Prolamins are the major seed storage proteins of species of the grass tribeAndropogonea. They are unusually rich in glutamine, proline, alanine, and leucine residues and their sequences show a series of tandem repeats presumed to be the result of multiple intragenic duplication. Two new sequences of α‐prolamin clones fromCoix(pBCX25.12 and pBCX25.10) are compared with similar clones from maize andSorghumin order to investigate evolutionary relationships between the repeat motifs and to propose a schematic model for their three‐dimensional structure based on hydrophobic membrane‐helix propensities and helical “wheels.” A scheme is proposed for the most recent events in the evolution of the central part of the molecule (repeats 3 to 8) which involves two partial intragenic duplications and in which contemporary odd‐numbered and even‐numbered repeats arise from common ancestors, respectively. Each pair of repeats is proposed to form an antiparallel α‐helical hairpin and that the helices of the molecule as a whole are arranged on a hexagonal net. The majority of helices show six faces of alternating hydrophobic and polar residues, which give rise to intersticial holes around each helix which alternate in chemical character. The model is consistent with proteins which contain different numbers of repeats, with oligomerization and with the dense packaging of α‐prolamins within the protein body of the seed endosperm.

ISSN:0887-3585    

DOI:10.1002/prot.340150111

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

年代:1993

数据来源: WILEY