The determination of the three-dimensional structure of barley serine proteinase inhibitor 2 by nuclear magnetic resonance, distance geometry and restrained molecular dynamics

The solution structure of the 64 residue structured domain (residues20–83) of barley serine proteinase inhibitor 2 (BSPI-2)is determined on the basis of 403 interproton distance, 34 øbackbone torsion angle and 26 hydrogen bonding restraints derivedfrom n.m.r. measurements. A total of 11 converged structureswere computed using a metric matrix distance geometry algorithmand refined by restrained molecular dynamics. The average rmsdifference between the final 11 structures and the mean structureobtained by averaging their coordinates is 1.4±0.2 Åfor the backbone atoms and 2.1±0.1 A for all atoms. Theoverall structure, which is almost identical to that found byX-ray crystallography, is disc shaped and consists of a centralfour component mixed parallel and antiparallel ß-sheetflanked by a 13 residue helix on one side and the reactivesite loop on the other.     

Comparison of the solution and X-ray structures of barley serine proteinase inhibitor 2

A comparison of the solution n.m.r. structures of barley serineprotease inhibitor 2 (BSPI-2) with the X-ray structures of bothsubtilisin complexed and native BSPI-2 is presented. It is shownthat the n.m.r. and X-ray structures are very similar in termsof overall shape, size, polypeptide fold and secondary structure.The average atomic rms difference between the 11 restraineddynamics structures on the one hand and the two X-ray structureson the other is 1.9±0.2 Å for the backbone atomsand 3.0±0.3 Å for all atoms. The cor respondingvalues for the restrained energy minimized mean dynamics structureare 1.5 and 2.4 Å, respectively.     

{beta}-sheet folding of fragment (16-36) of bovine pancreatic trypsin inhibitor as predicted by Monte Carlo simulated annealing

A tertiary structure prediction is described using Monte Carlosimulated annealing for the peptide fragment corresponding toresidues 16–36 of bovine pancreatic trypsin inhibitor(BPTI). The simulation starts with randomly chosen initial conformationsand is performed without imposing experimental constraints usingenergy functions given for generic interatomic interactions.Out of 20 simulation trials, seven conformations show a sheet-likestructure—two strands connected by a turn—althoughthis sheet-like structure is not as rigid as that observed innative BPTI. It is also shown that these conformations are mostlylooped and exhibit a native- like right-handed twist. Unlikethe case with the C-peptide of RNase A, no conspicuous -helicalstructure is found in any of the final conformations obtainedin the simulation. However, the lowest-energy conformation doesnot resemble exactly the native structure. This indicates thatthe rigid ß-sheet conformation of native BPTI merelycorresponds to a local minimum of the energy function if thefragment with residues 16–36 is isolated from the nativeprotein. A statistical analysis of all 20 final conformationssuggests that the tendency for the peptide segments to formextended ß-strands is strong for those with residues18–24, and moderate for those with residues 30–35.The segment of residues 25–29 does not tend to form anydefinite structure. In native BPTI, the former segments areinvolved in the ß-sheet and the latter in the turn.A folding scenario is also speculated from this analysis.     

Investigation of the solution structure of chymotrypsin inhibitor 2 using molecular dynamics: comparison to X-ray crystallographic and NMR data

The native solution structure and dynamics of chymotrypsin inhibitor2 (CI2) have been studied using a long (5.3 ns) molecular dynamics(MD) simulation without any imposed restraints. The majorityof the experimentally observed spin–spin coupling constants,short– and long–range nuclear Overhauser effect(NOE) cross peaks and the amide hydrogen exchange behavior werereproduced by the MD simulation. This good correspondence suggeststhat the major structural features of the protein during thesimulation are representative of the true protein structurein solution. Two water molecules formed hydrogen bond bridgesbetween ß₂ and ß₃, in agreement with X–raycrystallographic data and a recent reassessment of the solutionstructure using time averaged NMR restraints during MD refinement.The active–site loop of the protein displayed the greateststructural changes and the highest mobility. When this loopregion was excluded, the average C r.m.s. deviation of the simulatedsolution structures from the crystal structure was 1.5 from0.5 to 5 3 ns. There is structural heterogeneity in particularregions of the NMR–derived solution structures, whichcould be a result of imprecision or true internal motion. Astudy of the distribution of mobility through the protein allowsus to distinguish between these two alternatives. In particular,deviations in the active–site loop appear to be a resultof heightened mobility, which is also supported by good correspondencebetween calculated and experimental S² N–H order parameters.On the other hand, other ill–defined regions of the NMR-derivedstructures are well defined in the simulation and are probablythe result of a lack of structural restraints (i.e. NOEs), asopposed to reflecting the true mobility.     

Incorporation of an unnatural amino acid in the active site of porcine pancreatic phospholipase A2. Substitution of histidine by l,2,4-triazole-3-alanine yields an enzyme with high activity at acidic pH

The effect of the substitution of the active site histidine48 by the unnatural 1,2,4-triazole-3-alanine (TAA) amino acidanalogue in porcine pancreas phospholipase A₂ (PLA₂) was studied.TAA was introduced biosynthetically using a his-auxotrophicEscherichia coli strain. To study solely the effect of the substitutionof the active site histidine, two nonessential histidines (i.e.His17 and His 115) were replaced by asparagines, resulting ina fully active mutant enzyme (His-PLA₂). In this His-PLA₂ thesingle histidine at position 48 was substituted by TAA withan incorporation efficiency of about 90%, giving a mixture ofHis-PLA₂ and TAA-PLA₂. Based on the charge difference at acidicpH, both forms could be separated by FPLC, allowing for thepurification of TAA-PLA₂ free from His-PLA₂. At pH 6, TAA-PLA₂has a fivefold reduced activity compared with His-PLA₂. Thisreduced activity paralells a reduced rate of covalent modificationwith p-nitrophenacyl bromide of TAA-PLA₂ compared with His-PLA₂.Competitive inhibition gave comparable IC₅₀ values for WT-PLA₂,His-PLA₂ and TAA-PLA₂. These results indicate that the reductionin activity is not caused by a different affinity for the substrate,but more likely results from a reduced k_cat value in TAA-PLA₂.The enzymatic activities for native and mutant PLA₂s were measuredat different pH values. For WT-PLA₂ and His-PLA₂ the activityis optimal at pH 6 and is strongly deminished at acidic pH,with no observable activity at pH 3. In contrast, TAA-PLA₂ isas active at pH 3 as at pH 6. Most likely, the decrease in activityobserved for WT-PLA₂ and His-PLA₂ is caused by the protonationof the active site His48, which is the general base involvedin the activation of the nucleophilic water molecule. In TAA-PLA₂,however, the active site residue TAA48 is unprotonated at bothpH 3 and 6 as a result of the low pK_a of TAA compared with histidine.