X-ray crystallographic analysis of pokeweed antiviral protein-II after reductive methylation of lysine residues.

Pokeweed antiviral protein II (PAP-II) is a naturally occurring protein isolated from early summer leaves of the pokeweed plant (Phytolacca americana). PAP-II belongs to a family of ribosome-inactivating proteins which catalytically deadenylate ribosomal and viral RNA. The chemical modification of PAP-II by reductive methylation of its lysine residues significantly improved the crystal quality for X-ray diffraction studies. Hexagonal crystals of the modified PAP-II, with unit cell parameters a = b = 92.51 A, c = 79.05 A, were obtained using 1.8 M Na/K phosphate as the precipitant. These crystals contained one enzyme molecule per asymmetric unit and diffracted up to 2.4 A, when exposed to a synchroton source.

Modeling and alanine scanning mutagenesis studies of recombinant pokeweed antiviral protein.

The Phytolacca americana-derived naturally occurring ribosome inhibitory protein pokeweed antiviral protein (PAP) is an N-glycosidase that catalytically removes a specific adenine residue from the stem loop of ribosomal RNA. We have employed molecular modeling studies using a novel model of PAP-RNA complexes and site-directed mutagenesis combined with bioassays to evaluate the importance of the residues at the catalytic site and a putative RNA binding active center cleft between the catalytic site and C-terminal domain for the enzymatic deadenylation of ribosomal RNA by PAP. As anticipated, alanine substitutions by site-directed mutagenesis of the PAP active site residues Tyr(72), Tyr(123), Glu(176), and Arg(179) that directly participate in the catalytic deadenylation of RNA resulted in greater than 3 logs of loss in depurinating and ribosome inhibitory activity. Similarly, alanine substitution of the conserved active site residue Trp(208), which results in the loss of stabilizing hydrophobic interactions with the ribose as well as a hydrogen bond to the phosphate backbone of the RNA substrate, caused greater than 3 logs of loss in enzymatic activity. By comparison, alanine substitutions of residues (28)KD(29), (80)FE(81), (111)SR(112), (166)FL(167) that are distant from the active site did not significantly reduce the enzymatic activity of PAP. Our modeling studies predicted that the residues of the active center cleft could via electrostatic interactions contribute to both the correct orientation and stable binding of the substrate RNA molecule in the active site pocket. Notably, alanine substitutions of the highly conserved, charged, and polar residues of the active site cleft including (48)KY(49), (67)RR(68), (69)NN(70), and (90)FND(92) substantially reduced the depurinating and ribosome inhibitory activity of PAP. These results provide unprecedented evidence that besides the active site residues of PAP, the conserved, charged, and polar side chains located at its active center cleft also play a critical role in the PAP-mediated depurination of ribosomal RNA.

X-ray crystallographic analysis of the structural basis for the interaction of pokeweed antiviral protein with guanine residues of ribosomal RNA.

Pokeweed antiviral protein (PAP) is a ribosome-inactivating protein (RIP), which enzymatically removes a single adenine base from a conserved, surface exposed loop sequence of ribosomal rRNA. We now present unprecedented experimental evidence that PAP can release not only adenine but guanine as well from Escherichia coli rRNA, albeit at a rate 20 times slower than for adenine. We also report X-ray structure analysis and supporting modeling studies for the interactions of PAP with guanine. Our modeling studies indicated that PAP can accommodate a guanine base in the active site pocket without large conformational changes. This prediction was experimentally confirmed, since a guanine base was visible in the active site pocket of the crystal structure of the PAP-guanine complex.

X-ray crystallographic analysis of the structural basis for the interactions of pokeweed antiviral protein with its active site inhibitor and ribosomal RNA substrate analogs.

The pokeweed antiviral protein (PAP) belongs to a family of ribosome-inactivating proteins (RIP), which depurinate ribosomal RNA through their site-specific N-glycosidase activity. We report low temperature, three-dimensional structures of PAP co-crystallized with adenyl-guanosine (ApG) and adenyl-cytosine-cytosine (ApCpC). Crystal structures of 2.0-2.1 A resolution revealed that both ApG or ApCpC nucleotides are cleaved by PAP, leaving only the adenine base clearly visible in the active site pocket of PAP. ApCpC does not resemble any known natural substrate for any ribosome-inactivating proteins and its cleavage by PAP provides unprecedented evidence for a broad spectrum N-glycosidase activity of PAP toward adenine-containing single stranded RNA. We also report the analysis of a 2.1 A crystal structure of PAP complexed with the RIP inhibitor pteoric acid. The pterin ring is strongly bound in the active site, forming four hydrogen bonds with active site residues and one hydrogen bond with the coordinated water molecule. The second 180 degrees rotation conformation of pterin ring can form only three hydrogen bonds in the active site and is less energetically favorable. The benzoate moiety is parallel to the protein surface of PAP and forms only one hydrogen bond with the guanido group of Arg135.

Deguanylation of human immunodeficiency virus (HIV-1) RNA by recombinant pokeweed antiviral protein.

Modeling studies, combined with the molecular docking of the trinucleotide GGG into the active site of the deadenylating RNA N-glycosidase pokeweed antiviral protein (PAP), indicated that a guanine base can fit into the active site pocket of PAP without disturbing its unique geometry and is sandwiched between residues Tyr(72) and Tyr(123) very much like an adenine base. The guanine base can form two specific hydrogen bonds with the active site residues Ser(121) and Val(73) and the attached negatively charged phosphate groups can entertain stabilizing electrostatic interactions with two clusters of positively charged patches on the PAP surface formed by Lys(210) and Arg(179) from one side and Arg(122) and Arg(135) from the other side of the active site. These observations prompted the hypothesis that the RNA depurinating activity of PAP may not be restricted to adenine residues and PAP should be capable of deguanylating ribosomal and viral RNA as well. This hypothesis was experimentally confirmed by direct demonstration that guanine base is released from both ribosomal and HIV-1 RNA after treatment with purified recombinant PAP using quantitative high performance liquid chromatography. Recombinant PAP released adenine and guanine residues at a 1:1 ratio from HIV-1 RNA and at an approximately 3:1 (adenine:guanine) ratio from Escherichia coli ribosomal RNA. At a concentration of 5 microM, recombinant PAP released 263 +/- 10 pmol of adenine and 100 +/- 11 pmol of guanine from 1 microgram of E. coli ribosomal RNA (16S + 23S) within 4 h of treatment. By comparison, 138 +/- 12 pmol of adenine and 143 +/- 10 pmol of guanine were released from 1 microgram of HIV-1 RNA under identical treatment conditions (5 microM recombinant PAP, 4 h treatment). The deguanylation of the ribosomal and viral RNA targets by recombinant PAP was concentration-dependent and is abolished by alanine substitutions of the catalytic active site residues Tyr(72) and Tyr(123). To our knowledge, these findings provide the first evidence that PAP can deguanylate both ribosomal and viral RNA.

[Comparison of dynamic properties of various globular proteins and polyglutamic acid in alpha-helical and coil states. Rayleigh scattering of Mossbauer radiation data]. / Sravnenie dinamicheskikh svoistv razlichnykh globuliarnykh belkov i poliglutaminovoi kisloty v sostoianii alpha-spirali i klubka. Dannye réleevskogo rasseianiia Messbauérovskogo izlucheniia.

Classical model system: Poly-L-glutamic acid (Poly-Glu) was investigated in a disordered coil state (at pH-7.0) and in helix state (at pH 2.0) by Rayleigh scattering of Moessbauer radiation technique. Consider that the coil state of poly-Glu models unfolded (random coil) state and alpha-helix state models the fluctuating secondary structure (during consequent folding of protein) comparative analysis of dynamical properties of poly-Glu in different states with dynamical properties of different proteins in native state (alpha-helical myoglobin and HSA, partially beta-sheet lysozyme) and in intermediate (molten globule) state (alpha-lactalbumin) was performed. This comparison bring some surprising results: native alpha-helical proteins behave itself close to random coil, native partially beta-sheet protein behaves close to fluctuating secondary structure (alpha-helix) and the dynamic behaviour of molten globule state (partially beta-sheet alpha-lactalbumin) is not different from those behaviour of lysozyme and much more rigid than native alpha-helical proteins. As a result one cannot exclude the possibility that folding process and dynamical properties at different steps of the folding are very different for alpha-helical and beta-sheet proteins.

Two crystal structures of the leupeptin-trypsin complex.

Three-dimensional structures of trypsin with the reversible inhibitor leupeptin have been determined in two different crystal forms. The first structure was determined at 1.7 A resolution with R-factor = 17.7% in the trigonal crystal space group P3(1)21, with unit cell dimensions of a = b = 55.62 A, c = 110.51 A. The second structure was determined at a resolution of 1.8 A with R-factor = 17.5% in the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 63.69 A, b = 69.37 A, c = 63.01 A. The overall protein structure is very similar in both crystal forms, with RMS difference for main-chain atoms of 0.27 A. The leupeptin backbone forms four hydrogen bonds with trypsin and a fifth hydrogen bond interaction is mediated by a water molecule. The aldehyde carbonyl of leupeptin forms a covalent bond of 1.42 A length with side-chain oxygen of Ser-195 in the active site. The reaction of trypsin with leupeptin proceeds through the formation of stable tetrahedral complex in which the hemiacetal oxygen atom is pointing out of the oxyanion hole and forming a hydrogen bond with His-57.

The influence of temperature on lysozyme crystals. Structure and dynamics of protein and water.

Lysozyme structures at six different temperatures in the range 95-295 K have been determined using X-ray crystallography at a resolution of 1.7 A. The crystals at lower temperatures had a 7.4% decrease in the unit-cell volume. The volume change was discontinuous with the volume being near 238 000 A(3) from 295 to 250 K and about 220 200 A(3) below 180 K. The thermal expansion of the protein has been analyzed and shows anisotropy, which is correlated with local atomic packing and secondary-structure elements. The lysozyme structure at low temperature is nearly the same as that at high temperature, with only small relative translations and rotations of structure elements including a hinge-bending rearrangement of two domains. Because of a considerable increase of lattice disorder at low temperature dynamical analysis of internal motion is difficult. The analysis of structural and dynamical properties of well ordered protein-bound water has been carried out.

Prediction of new serine proteinase inhibitors.

We describe here the use of a rapid computational method to predict the relative binding strengths of a series of small-molecule ligands for the serine proteinase trypsin. Flexible molecular models of the ligands were docked to the proteinase using an all-atom potential set, without cutoff limits for the non-bonded and electrostatic energies. The binding-strength calculation is done directly in terms of a molecular mechanics potential. The binding of eighteen different compounds, including non-binding controls, has been successfully predicted. The measured Ki is correlated with the predicted energy. The correctness of the theoretical calculations is demonstrated with both kinetics measurements and X-ray structure determination of six enzyme-inhibitor complexes.

[Study of the dynamics of human serum albumin by coherent Rayleigh dispersion of Mossbauer radiation]. / Izuchenie dinamiki syvorotochnogo al'bumina cheloveka metodom kogerentnogo réleevskogo rasseianiia Messbauérovskogo izlucheniia.

The measurements of angle dependencies of total and elastic Rayleigh scattering of Mossbauer radiation intensities have been performed for human serum albumin (HSA) with hydration degrees h = 0.13 and h = 0.4. The extended model was developed for calculating the inelastic intensity of Rayleigh scattering. Original data for HSA and published data on met-Mb were fitted within the frame of this model. The best agreement with experiment was obtained when two types of intraglobular motions were taken into account: individual motions of small side-chain groups and cooperative (mechanical) motions of segments (most probable alpha-helices). Long-range correlated motions are essential at low hydration degree. The possibilities of application of the coherent version of RSMS technique are described.

[Evaluation of the contribution of various types of movement of protein globules into effects observed using the Rayleigh scattering of Mössbauer radiation or the Mössbauer absorption spectroscopy]. / Otsenka vkladov raznykh vidov dvizheniia globul belka v éffekty, nabliudaemye s pomoshch'iu releevskogo rasseianiia messbauérovskogo izlucheniia i messbauérovskoi absorbtsionnoi spektroskopii.

Conditions (regions of hydration degrees and temperatures) are considered at which effects observed in Rayleigh Scattering of Mössbauer Radiation and Mössbauer Absorption Spectroscopy can be attributed to changes in intramolecular mobility, rather than contribution of different types of motions of macromolecules as a whole.

[A study of the effect of solvent composition and viscosity on the molecular dynamics of human serum albumin using Rayleigh scattering of Mössbauer radiation]. / Izuchenie vliianiia sostava i viazkosti rastvoritelia na molekuliarnuiu dinamiku syvorotochnogo al'bumina cheloveka metodom releevskogo rasseianiia messbauérovskogo izlucheniia.

By means of RSMR changes of human serum albumen intramolecular mobility by addition of 1.5% and 7.5% of glutar dialdehyde (GD) in concentrated protein solution, heat denaturation of a protein or substitution of water by water-glycerol solvent with amount of water to glycerol: 1 to 2 were studied. It is shown that the elastic fraction for HSA is changed much less addition of GD or by heat denaturation than by substitution of water solution by water-glycerol. It seems that the observed strong influence of glycerol on intramolecular mobility of HSA is connected mostly with effective dehydration of protein (by substitution of the part of a water solvent by glycerol) and with a small volume decrease of protein (due to preference hydration effect) rather than with the increase of the solvent viscosity.

[Study of protein dynamics using Mössbauer spectroscopy]. / Issledovanie dinamiki belkov metodami messbauérovskoi spektroskopii.

Last experimental results of the study of protein dynamics by Mössbauer absorption spectroscopy and Rayleigh scattering of Mössbauer radiation are reviewed. Dynamical properties of proteins following from the theoretical treatment of these data are described.

[Study of the effect of hydration on the dynamics of various globular proteins by Rayleigh scattering of Mössbauer radiation]. / Izuchenie vliianiia gidratatsii na dinamiku nekotorykh globuliarnykh belkov metodom réleevskogo rasseianiia messbauérovskogo izlucheniia.

Hydration relationships of the elastic scattering fraction of Mössbauer radiation were studied for human serum albumin (HSA), pancreatic trypsin inhibitor and lysozyme within hydration degrees 0 less than or equal to h less than or equal to 0.75 g/g (at T = 295 degrees K) and temperatures 100K less than or equal to T less than or equal to 320 K (for HSA only at h = 0.03; 0.25; 0.41; 0.65). It is shown that the increase of both hydration degree above h greater than 0.1 and temperature above T greater than 200K leads to the appearance of intramolecular mobility in these proteins.