摘要:

AbstractThe structure of the complex between cyclosporin A and the Fab fragment of a monoclonal antibody has been established by Crystallographic analysis to 2.65 Åresolution. The structure has been solved by molecular replacement using a composite Fab model. The currentR‐factor after refinement is 0.179 between 8 and 2.65Åresolution. The antibody is one among three known structures with long H3 loops. This loop conformation is observed for the first tune in the presence of the antigen. Residues from all six hypervariable loops interact with cyclosporin A. However, the 17 residues long loop H3 is the main contributor to the buried combining site area and to the van der Waals contacts made with cyclosporin A, with 52 and 63%, respectively, of the total contribution. © 1993 Wiley‐Lis

ISSN:0887-3585    

DOI:10.1002/prot.340150402

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

年代:1993

数据来源: WILEY

摘要:

AbstractIn a recent classification of biologically active amphipathic α‐helixes, the lipid‐associating domains in exchangeable plasma apolipoproteins have been classified as class A amphipathic helixes (Segrest, J. P., De Loof, H., Dohlman, J. G., Brouillette, C. G., Anantharamaiah, G. M.Proteins8:103–117, 1990). A model peptide analog with the sequence, Asp Trp Leu Lys Ala Phe Tyr Asp Lys Val Ala Glu Lys Leu Lys Glu Ala Phe (18A), possesses the characteristics of a class A amphipathic helix. The addition of an acetyl group at the α‐amino terminus and an amide at the α‐carboxyl terminus, to obtain Ac‐18A‐NH2, produces large increases in helicity for the peptide both in solution and when associated with lipid (for 18A vs Ac‐18A‐NH2, from 6 to 38% helix in buffer and from 49 to 92% helix when bound to dimyristoyl phosphatidylcholine in discoidal complexes). Blocking of the end‐groups of 18A stabilizes the α‐helix in the presence of lipid by approximately 1.3 kcal/mol. There is also an increase in the self‐association of the blocked peptide in aqueous solution. The free energy of binding to the PC–water interface is increased only by about 3% (from −8.0 kcal/mol for 18A to −8.3 kcal/mol for Ac‐18A‐NH2). The Ac‐18A‐NH2has a much greater potency in raising the bilayer to hexagonal phase transition temperature of dipalmitoleoyl phosphatidylethanolamine than does 18A. In this regard Ac‐18A‐NH2more closely resembles the behavior of the apolipoprotein A‐I, which is the major protein component of high‐density lipoprotein and a potent inhibitor of lipid hexagonal phase formation. The activation of the plasma enzyme lecithin: cholesterol acyltransferase by the Ac‐18A‐NH2peptide is greater than the 18A analog and comparable to that observed with the apo A‐I. In the case of Ac‐18A‐NH2, the higher activating potency may be due, at least in part, to the ability of the p

ISSN:0887-3585    

DOI:10.1002/prot.340150403

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe dynamic properties of the RNase A/3′–UMP enzyme/product complex and the S‐peptide of RNase A have been investigated by molecular dynamics simulations using suitable generalization of ideas introduced to probe the energy landscape in structural glasses. We introduce two measures, namely, the kinetic energy fluctuation metric and the force metric, both of which are used to calculate the time needed for sampling the conformation space of the molecules. The calculation of the fluctuation metric requires a single trajectory whereas the force metric is computed using twoindependenttrajectories. The vacuum MD simulations show that for both systems the time required for kinetic energy equipartitioning is surprisingly long even at high temperatures. We show that the force metric is a powerful means of probing the nature and relative importance of conformational substates which determine the dynamics at low temperatures. In particular the time dependence of the non‐bonded force metric is used to demonstrate that at low temperatures the system is predominantly localized hi a single cluster of conformational substates. The force metric is used to show that relaxation of long range (in sequence space) interactions must be mediated by a sequence of local dihedral angle transitions. We also argue that the time needed for compact structure formation is intimately related to the time needed for the relaxation of the dihedral angle degrees of freedom. The tame for non‐bonded interactions, which drive protein molecules to fold under appropriate conditions, to relax becomes extremely long as the temperature is lowered suggesting that the formation of maximally compact structure hi proteins must be a very slow process. © 1993 Wiley

ISSN:0887-3585    

DOI:10.1002/prot.340150404

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe dynamic behavior of one 99‐residue subunit of the dimeric aspartyl protease of HIV‐1 was studied in a 160 psec molecular dynamics simulation at 300 K in water. The crystal structure of one of the identical subunits of the dimer was the starting point, with the aqueous phase modeled by 4,331 explicit waters in a restrained spherical droplet Analysis of the simulations showed that the monomer displayed considerable flexibility in the interfacial portions of the flap (the region which folds over the substrate), the N‐ and C‐0termini, and, to a lesser extent, the active site. The flap undergoes significant motion as an independent rigid finger, but without the cantilever previously reported hi a simulation of the dimer. The N‐terminus displayed the greatest fluctuational disorder whereas the C‐terminus exhibited the greatest root mean square movement from the crystal structure. The central core of the monomer had a heavy‐atom root mean square deviation from the initial structure of about 3.0 Å during the latter half of the simulation. Although this is larger than the 1.6 Å found for comparable simulations of typical globular proteins, the general features of the tertiary structure were preserved over the course of the simulation. Overall, these results indicate that therelaxedstructure obtained in these simulations may provide a better model for the tertiary structure of the solvated HIV‐1 protease monomer than the subunit conformation seen in the X‐ray crystallographic structure of the dimer. Except in the flap region, the design of compounds intended to interfere with dimerization should take this relaxation and the flexibility of the solvated monomer, especially at the termini, into account. ©

ISSN:0887-3585    

DOI:10.1002/prot.340150405

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

年代:1993

数据来源: WILEY

摘要:

AbstractThe structure in solution of crambin, a small protein of 46 residues, has been determined from 2D NMR data using an iterative relaxation matrix approach (IRMA) together with distance geometry, distance bound driven dynamics, molecular dynamics, and energy minimization. A new protocol based on an “ensemble” approach is proposed and compared to the more standard initial rate analysis approach and a “single structure” relaxation matrix approach. The effects of fast local motions are included andR‐factor calculations are performed on NOE build‐ups to describe the quality of agreement between theory and experiment. A new method for stereospecific assignment of prochiral groups, based on a comparison of theoretical and experimental NOE intensities, has been applied. The solution structure of crambin could be determined with a precision (rmsd from the average structure) of 0.7 Å on backbone atoms and 1.1 Å on all heavy atoms and is largely similar to the crystal structure with a small difference observed in the position of the side chain of Tyr‐29 which is determined in solution by bothJ‐coupling and NOE data. Regions of higher structural variability (suggesting higher mobility) are found hi the solution structure, in particular for the loop between the two helices (Gly‐20 to Pro‐22).

ISSN:0887-3585    

DOI:10.1002/prot.340150406

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

年代:1993

数据来源: WILEY

摘要:

AbstractIn order to correlate between spectroscopic and structural changes in a protein, the environment of Trp 135 in T4 lysozyme was deliberately perturbed by the replacement of Gln 105 with alanine (Q105A), glycine (Q105G), and glutamic acid (Q105E). In wild‐type lysozyme, Trp 135 is buried, but the indole nitrogen is hydrogen‐bonded to the side‐chain of Gln 105. In the Q105G and Q105A mutant structures, the indole nitrogen becomes accessible to solvent. Crystallographic analysis shows that the structures of all of the mutants are similar to wild‐type. There are, however, distinct rearrangements of the local solvent structure in response to the new side‐chains. There are also small but significant changes in the relative orientations of the two domains of the protein that appear to result from a series of small, concerted movements of side‐chains adjacent to residue 105. Evaluation of the fluorescence and phosphorescence of the mutant proteins in terms of their observed three‐dimensional structures shows that large spectral changes do not necessarily imply large changes in structure or in static solvent accessibility. Increases in polar relaxation about the excited state of tryptophan may be the result of only small increases in local dynamics or solvent exposure.1H‐NMR was also used to monitor the effects of the substitutions on Trp 138. In Q105E, but not in Q105G, Q105A and WT, the Hε1chemical shift of Trp 138 is very pH‐dependent, apparently reflecting the titration of Glu 105 which has a spectroscopically determined pKaof 6.0. The elevation of the pKaof Glu 105 in Q105E is also reflected in the pH dependence of the stability of this mutant. © 1

ISSN:0887-3585    

DOI:10.1002/prot.340150407

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

年代:1993

数据来源: WILEY

摘要:

AbstractWe present a novel search strategy for determining the optimal packing of protein secondary structure elements. The approach is based on conformational energy optimization using a predetermined set of side chain rotamers and appropriate methods for sampling the conformational space of peptide fragments having fixed backbone geometries. An application to the 4‐helix bundle of myohemerythrin is presented. It is shown that the conformations of the amino acid side chains are largely determined at the level of helix pairs and that superposition of these results can be used to construct the full bundle. The final solution obtained, taking into account restrictions due to the lateral amphiphilicity of the helices, differs from the native structure by only a 20° rotation of a single helix. © 1993 Wiley‐Liss

ISSN:0887-3585    

DOI:10.1002/prot.340150408

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

年代:1993

数据来源: WILEY

摘要:

AbstractMolecular dynamics simulation and free energy perturbation techniques have been used to study the relative binding free energies of the designed mechanism‐based pterins, 8‐methylpterin and 6,8‐dimethylpterin, to dihydrofolate reductase (DHFR), with co‐factor nicotinamide adenine dinucleotide phosphate (NADPH). The calculated free energy differences suggest that DHFR.NADPH.6,8‐dimethylpterin is thermodynamically more stable than DHFR.NADPH.8‐methylpterin by 2.4 kcal/mol when the substrates are protonated and by 1.3 kcal/mol when neutral. The greater binding strength of 6,8‐dimethylpterin may be attributed largely to hydration effects. In terms of an appropriate model for the pH‐dependent kinetic mechanism, these differences can be interpreted consistently with experimental data obtained from previous kinetic studies, i.e., 6,8‐dimethylpterin is a more efficient substrate of vertebrate DHFRs than 8‐methylpterin. The kinetic data suggest a value of 6.6 ± 0.2 for the pKaof the active site Glu‐30 in DHFR.NADPH. We have also used experimental data to estimate absolute values for thermodynamic dissociation constants of the active (i.e., protonated) forms of the substrates: these are of the same order as for the binding of folate (0.1–10 μM). The relative binding free energy calculated from the empirically derived dissociation constants for the protonated forms of 8‐methylpterin and 6,8‐dimethylpterin is 1.4 kcal/mol, a value which compares reasonably well with the theoretical value of 2.4 kca

ISSN:0887-3585    

DOI:10.1002/prot.340150409

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

年代:1993

数据来源: WILEY

摘要:

AbstractA Monte Carlo algorithm that searches for the optimal docking configuration of hen egg white lysozyme to an antibody is developed. Both the lysozyme and the antibody are kept rigid. Unlike the work of other authors, our algorithm does not attempt to explicitly maximize surface contact, but minimizes the energy computed using coarse‐grained pair potentials. The final refinement of our best solutions using all‐atom OPLS potentials (Jorgensen and Tirado‐Rives8) consistently yields the native conformation as the preferred solution for three different antibodies. We find that the use of an exponential distance‐dependent dielectric function is an improvement over the more commonly used linear form. © 1993 Wiley

ISSN:0887-3585    

DOI:10.1002/prot.340150410

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

年代:1993

数据来源: WILEY

ISSN:0887-3585    

DOI:10.1002/prot.340150401

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

年代:1993

数据来源: WILEY