Predicting Differential Antigen–Antibody Contact Regions Based on Solvent Accessibility

A novel computational approach was examined tor predicting epitopes from primary structures of the seven immunologically distinct botulinum neurotoxins (BoNT/A-G) and tetanus toxin (TeTX). An artificial neural network [Rost and Sander (1994), Proteins 20, 216] was used to estimate residue solvent accessibilities in multiple aligned sequences. A similar network trained to predict secondary structures was also used to examine this protein family, whose tertiary fold is presently unknown. The algorithm was validated by showing that it was 80% accurate in determining the secondary structure of avian egg-white lysozyme and that it correctly identified highly solvent-exposed residues that correspond to the major contact regions of lysozyme–antibody cocrystals. When sequences of the heavy (H) chains of TeTX and BoNT/A–G were analyzed, this algorithm predicted that the most highly exposed regions were clustered at the sequentially nonconserved N- and C-termini [Lebeda and Olson (1994), Proteins 20, 293]. The secondary structures and the remaining highly solvent-accessible regions were, in contrast, predicted to be conserved. In experiments reported by others, H-chain fragments that induced immunological protection against BoNT/A overlap with these predicted most highly exposed regions. It is also known that the C-terminal halves of the TeTX and BoNT/A H-chains interfere with holotoxin binding to ectoacceptors on nerve endings. Thus, the present results provide a theoretical framework for predicting the sites that could assist in the development of genetically engineered vaccines and that could interact with neurally located toxin ectoacceptors. Finally, because the most highly solvent-exposed regions were not well conserved, it is hypothesized that nonconserved, potential contact sites partially account for the existence of different dominant binding regions for type-specific neutralizing antibodies.     

Assignments of1H−15N magnetic resonances and identification of secondary structure elements of the λ-cro repressor

Summary The assignments of¹H–¹⁵N magnetic resonances of the -cro repressor are presented. Individual¹⁵N-amino acids were incorporated into the protein, or it was uniformly labeled with¹⁵N. For the¹³C–¹⁵N double-labeling experiments,¹³C-amino acids were incorporated into the uniformly¹⁵N-labeled protein. All the amide¹H–¹⁵N resonances could be assigned with such specific labeling, and sequential connectivities obtained by two-dimensional (2D)¹H–¹⁵N reverse correlation spectroscopies and three-dimensional (3D)¹H/¹⁵N NOESY-HMQC spectroscopy. Conventional 2D¹H–¹H correlation spectroscopies were applied to the assignment of the side-chain protons. Some of the¹H resonance assignments are inconsistent with those previously reported [Weber, P.L., Wemmer, D.E. and Reid, B.R. (1985)Biochemistry,24, 4553–4562]. The sequential NOE connectivities and H-D exchange rates indicate several elements of the secondary structure, including -helices consisting of residues 8–15, 19–25 and 28–37, and three extended strands consisting of residues 4–7, 39–45 and 49–55. Based on several long-range NOEs, the three extended strands could be combined to form an antiparallel -sheet. The amide proton resonances of the C-terminal residues except Ala⁶⁶ (residues 60–65) were hardly observed at neutral pH, indicating that the arm is flexible. The identified secondary structure elements in solution show good agreement with those in the crystal structure of the cro protein [Anderson, W.F., Ohlendorf, D.H., Takeda, Y. and Matthews, B.W. (1981)Nature,290, 754–758].     

Aliphatic 1H and 13C resonance assignments for the 26-10 antibody VL domain derived from heteronuclear multidimensional NMR spectroscopy

Summary Extensive ¹H and ¹³C assignments have been obtained for the aliphatic resonances of a uniformly ¹³C-and ¹⁵N-labeled recombinant V_L domain from the anti-digoxin antibody 26-10. Four-dimensional triple resonance NMR data acquired with the HNCAHA and HN(CO)CAHA pulse sequences [Kay et al. (1992) J. Magn. Reson., 98, 443–450] afforded assignments for the backbone H^N, N, H and C resonances. These data confirm and extend H^N, N and H assignments derived previously from three-dimensional ¹H-¹⁵N NMR studies of uniformly ¹⁵N-labeled V_L domain [Constantine et al. (1992), Biochemistry, 31, 5033–5043]. The identified H and C resonances provided a starting point for assigning the side-chain aliphatic ¹H and ¹³C resonances using three-dimensional HCCH-COSY and HCCH-TOCSY experiments [Clore et al. (1990), Biochemistry, 29, 8172–8184]. The C and C chemical shifts are correlated with the V_L domain secondary structure. The extensive set of side-chain assignments obtained will allow a detailed comparison to be made between the solution structure of the isolated V_L domain and the X-ray structure of the V_L domain within the 26–10 Fab.     

A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins

The three-dimensional structure of human angiogenin has been determined by X-ray crystallography and is compared here with an earlier model which predicted its structure, based on the homology of angiogenin with bovine pancreatic ribonuclease A. Comparison of the predicted model and crystal structure shows that the active-site histidine residues and the core of the angiogenin molecule, including most of the-strands and-helices, were predicted reasonably well. However, the structure of the surface loop regions and residues near the truncated C-terminus differs significantly. The C-terminal segment includes the active-site residues Asp-116, Gln-117, and Ser-118; Gln-117 in particular has been shown to be important in affecting the ribonucleolytic activity of angiogenin. Also, the orientation of one helix in the model differed from the orientation observed experimentally by about 20°, resulting in a large displacement of this chain segment. The difficulty encountered in predicting the surface loop regions has led to a new algorithm [Palmer and Scheraga (1991),J. Comput. Chem.,12, 505–526; (1992),J. Comput. Chem.,13, 329–350] for predicting the conformations of surface loops.     

Structure and dynamics of Candida rugosa lipase: the role of organic solvent

The effect of organic solvent on the structure and dynamics of proteins was investigated by multiple molecular dynamics simulations (1 ns each) of Candida rugosa lipase in water and in carbon tetrachloride. The choice of solvent had only a minor structural effect. For both solvents the open and the closed conformation of the lipase were near to their experimental X-ray structures (C rms deviation 1–1.3 Å). However, the solvents had a highly specific effect on the flexibility of solvent-exposed side chains: polar side chains were more flexible in water, but less flexible in organic solvent. In contrast, hydrophobic residues were more flexible in organic solvent, but less flexible in water. As a major effect solvent changed the dynamics of the lid, a mobile element involved in activation of the lipase, which fluctuated as a rigid body about its average position. While in water the deviations were about 1.6 Å, organic solvent reduced flexibility to 0.9 Å. This increase rigidity was caused by two salt bridges (Lys85–Asp284, Lys75–Asp79) and a stable hydrogen bond (Lys75–Asn 292) in organic solvent. Thus, organic solvents stabilize the lid but render the side chains in the hydrophobic substrate-binding site more mobile. Figure Superimposition of open (black, PDB entry 1CRL) and closed (gray, PDB entry 1TRH) conformers of C. rugosa lipase. The mobile lid is indicatedThis revised version was published online in October 2004 with corrections to the Graphical Abstract.     

Secondary structure of β-hydroxydecanoyl thiol ester dehydrase, a 39-kDa protein, derived from Hα, Cα, Cβ and CO signal assignments and the Chemical Shift Index: Comparison with the crystal structure

Summary Nearly complete backbone ¹H, ¹⁵N and ¹³C signal assignments are reported for -hydroxydecanoyl thiol ester dehydrase, a 39-kDa homodimer containing 342 amino acids. Although ¹⁵N relaxation data show that the protein has a rotational correlation time of 18 ns, assignments were derived from triple-resonance experiments recorded at 500 MHz and pH 6.8, without deuteration. The Chemical Shift Index, CSI, identified two long helices and numerous -strands in dehydrase. The CSI predictions are in close agreement with the secondary structure identified in the recently derived crystal structure, particularly when one takes account of the numerous bulges in the -strands. The assignment of dehydrase and a large deuterated protein [Yamazaki et al. (1994) J. Am. Chem. Soc., 116, 11655–11666] suggest that assignment of 40–60 kDa proteins is feasible. Hence, further progress in understanding the chemical shift/structure relationship could open the way to determine the structures of such large proteins. Supplementary Material is available on request, comprising Table S1 listing the spectral parameters; Table S2 listing the assignments; Fig. S1 showing the 2D ¹H–¹⁵N HSQC spectrum; Fig. S2 showing sequential NOEs, secondary shifts, H-exchange and ³J_HN data; and Fig. S3 showing plots of the H, C, CO and C Chemical Shift Indexes.To whom correspondence should be addressed.     

Enantioselective enzymatic acetylation of racemic [4-[4α,6β (E)]]-6-[4,4-bis(4-fluorophenyl)-3-(1-methyl-1H-tetrazol-5-yl)-1,3-butadienyl]-tetrahydro-4-hydroxy-2H-pyran-2-one

Summary A chiral compound [4R-[4,6ß(E)]]-6-[4,4-bis(4-fluorophenyl)-3-(1-methyl-1H-tetrazol-5-yl)-1,3-butadienyl]-tetrahydro-4-hydroxy-2H-pyran-2-one (R-(+)-1) was prepared by the lipase-catalysed stereoselective acetylation of racemic 1 in an organic solvent. Chiral R-(+)-1 is a hydroxymethyl glutaryl coenzyme A (HMG CoA) reductase inhibitor and a potential anticholesterol drug candidate. Among various lipases evaluated, lipase PS-30 from Pseudomonas species efficiently catalysed acetylation of the undesired enantiomer of racemic 1 to yield the S-(–)-acetylated product 2 and unreacted desired R-(+)-1. A reaction yield of 48 mol% and an optical purity of 98% were obtained for R-(+)-1 when the reaction was conducted in toluence as solvent in the presence of isopropenyl acetate as acyl donor. Lipase PS-30 was immobilized on Accurel polypropylene (PP) and the immobilized enzyme was reused (five cycles) in the acetylation reaction without loss of enzyme activity, productivity, or optical purity of the R-(+)-1. The enzymatic acetylation process was scaled-up to 501 and a 640-l volume (preparative batches) at a substrate concentration of 4 g/l. R-(+)–1 was recovered from the preparative batches in 68–71% recovery yield with 98.5% gas chromatography homogeneity index and 98.5% optical purity. The S-(–) acetate 2 produced by the acetylation reaction was enzymatically hydrolysed by lipase PS-30 in a biphasic system to prepare the corresponding S-(–)-1.Correspondence to: R. N. Patel     

Spatial structure of (34–65)bacterioopsin polypeptide in SDS micelles determined from nuclear magnetic resonance data

Summary The spatial structure of a synthetic 32-residue polypeptide, an analog of the membrane-spanning segment B (residues 34–65) of bacterioopsin ofHalobacterium halobium, incorporated into perdeuterated sodium dodecyl sulfate micelles, was determined from¹H NMR data. The structure determination included the following steps: (1) local sructure analysis; (2) structure calculations using the distance geometry program DIANA; (3) systematic search for energetically allowed side-chain rotamers consistent with NOESY crosspeak volumes; (4) random generation of peptide conformations in allowed conformational space. The obtained structure has a righ-handed -helicl region from Lys⁴¹ to Leu⁶² with a kink of 27 at Pro⁵⁰. The C-cap Gly⁶³ adopts a conformation with =87±6, =43±10^o typical to a left-handed helix. The N-terminal part (residues 34–40) is exposed to the aqueous phase and lacks an ordered conformation. The secondary structure of segment B in micelles is consistent with the high-resolution electron cryomicroscopy model of bacteriorhodopsin (Henderson et al. (1990)J. Mol. Biol.,213, 899–929).     

Modelling continuous culture of Rhodospirillum rubrum in photobioreactor under light limited conditions

Rhodospirillum rubrum was grown continuously and photoheterotrophically under light limitation using a cylindrical photobioreactor in which the steady state biomass concentration was varied between 0.4 to 4 kg m^–3 at a constant radiant incident flux of 100 W m^–2. Kinetic and stoichiometric models for the growth are proposed. The biomass productivities, acetate consumption rate and the CO₂ production rate can be quantitatively predicted to a high level of accuracy by the proposed model calculations. Nomenclature: C _X, biomass concentration (kg m^–3) D, dilution rate (h^–1) Ea, mean mass absorption coefficient (m² kg^–1) I , total available radiant light energy (W m^–2) K, half saturation constant for light (W m^–2) R _W, boundary radius defining the working illuminated volume (m) r _X, local biomass volumetric rate (kg m^–3 h^–1) <r _X>, mean volumetric growth rate (kg m^–3 h^–1) V _W, illuminated working volume in the PBR (m^–3). Greek letters: , working illuminated fraction (–) _M, maximum quantum yield (–) bar, mean energetic yield (kg J^–1).     

Toxin III of the scorpionAndroctonus australis Hector: Proton nuclear magnetic resonance assignments and secondary structure

Summary ¹H NMR has been applied to a3.5 mM, pH 5.4, solution of toxin III (64 amino acids) from venom of the scorpionAndroctonus australis Hector. The resonance assignment strategy began by applying a generalized main-chain directed method for rapid identification and resonance assignments of secondary structures. The remaining resonances were assigned by the sequential method. Major structural features include a helix of 2 1/2 turns (residues 20–28) which is linked by two disulfide bridges to the central strand of a triple-stranded antiparallel -sheet. Turns were identified at residues 15–17, 47–49 and also at residues 51–53. Numerous NOEs have been observed between hydrophobic residues which suggest the presence of a hydrophobic core; these include Leu³⁷, Leu²³, Val⁴⁷, Tyr¹⁴, Trp⁴⁵ and Tyr⁵. The Trp⁴⁵ and Tyr⁵ rings lie orthogonal to one another. No crystal structure has been solved for this AaH III toxin. Comparisons are made with other members of the scorpion toxin family.Thenomenclature used is similar to that described by Wütrich, 1986.     

Solution structure of a synthetic peptide corresponding to a receptor binding region of FSH (hFSH-beta 33-53).

The receptor binding surface of human follicle-stimulating hormone (hFSH) is mimicked by synthetic peptides corresponding to the hFSH- chain amino acid sequences 33–53 [Santa-Coloma, T. A., Dattatreyamurty, D., and Reichert, L. E., Jr. (1990),Biochemistry 29, 1194–1200], 81–95 [Santa-Coloma, T. A., and Reichert, L. E., Jr. (1990),J. Biol. Chem. 265, 5037–5042], and the combined sequence (33–53)–(81–95) [Santa-Coloma, T. A., Crabb, J. W., and Reichert, L. E., Jr. (1991),Mol. Cell. Endocrinol. 78, 197–204]. These peptides have been shown to inhibit binding of hFSH to its receptor. Circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy were used to determine the structure of the first peptide in this series, the 21 amino acid peptide hFSH--(33–53), H₂N-YTRDLVYKDPARPKIQKTCTF-COOH. Analysis of CD data indicated the presence of approximately equal amounts of antiparallel -pleated sheet, turns including a -turn, other structures, and a small amount ofa-helix. The major characteristics of the structure were found to be relatively stable at acidicpH and the predominant effect of increased solvent polarity was a small increase ina-helical content. One- and two-dimensional NMR techniques were used to obtain full proton and carbon signal assignments in aqueous solution atpH 3.1. Analysis of NMR results confirmed the presence of the structural features revealed by CD analysis and provided a detailed picture of the secondary structural elements and global folding pattern in hFSH--(33–53). These features included an antiparallel -sheet (residues 38–51 and 46–48), turns within residues 41–46, and 50–52 (a -turn) and a small N-terminal helical region comprised of amino acids 34–36. One of the turns is facilitated by prolines 42 and 45. Proline-45 was constrained to thetrans conformation, whereas proline-42 favored thetrans conformer (70%) over thecis (30%). Two resonances were observed for the single alanine residue (A-43) sequentially proximal to P-42, but the rest of the structure was minimally affected by the isomerization at proline-42. The major population of molecules, containingtrans-42 andtrans-45 prolines, presented 120 NOEs. Distance geometry calculations with 140 distance constraints and energy minimization refinements were used to derive a moderately well-defined model of the peptide's structure. The hFSH--(33–53) structure has a highly polar surface composed of six cationic amino acid (arginie-35, lysine-40, arginine-44, lysine-46, glutamine-48, and lysine-49) and two anionic residues (aspartate-36 and aspartic acid-41). A hydrophobic region in the structure is composed of residues in the antiparallel -sheet and -turn which fold to produce a distorted hairpin. The structure of this domain, together with the protruding and positively charged region in the vicinity of residues 42–45, may mimic the surface of hFSH that binds to the receptor.Abreviations used: hFSH, human follicle-stimulating hormone; PB, 25 mM Na₂KPO₄, 25 mM KH₂PO₄, and 5 mM Mg Cl₂; CD, circular dichroism spectrapolarimetry; NMR, nuclear magnetic resonance spectrometry; COSY, homonuclear correlated spectroscopy; NOESY, 2D nuclear Overhauser effect spectroscopy; HOHAHA, homonuclear Hartman-Han coherence transfer; HMQCHY, reverse-detected heteronuclear multiple shift correlation, one bond; HMBC, reverse-detected heteronuclear multiple bond correlation; S/N, signal to noise ratio; TFE, trifluoroethanol.Dr. Santa-Coloma is on leave of absence from the National Research Council of Argentina (CONICET).     

1H, 15N and 13C resonance assignments and monomeric structure of the amino-terminal extracellular domain of epithelial cadherin

Summary E-cadherin is a transmembrane protein that provides Ca²⁺-dependent cell adhesion to epithelial cells. The large majority of the ¹H, ¹⁵N, ¹³C and ¹³CO resonances of a 146-amino acid polypeptide from epithelial (E-) cadherin have been assigned using multidimensional NMR spectroscopy. The structure of the amino-terminal 100 amino acids, corresponding to the first extracellular repeat of E-cadherin [Overduin et al. (1995) Science, 267, 386–389], has been refined. The monomeric state of this isolated domain is demonstrated by light scattering and sedimentation analysis. Seven -strands and two short helices were identified by patterns of NOE cross-peaks, vicinal coupling constants and chemical shift indices. A novel structural motif termed a quasi--helix found in the crystal structure of a neural (N-) cadherin domain [Shapiro et al. (1995) Nature, 374, 327–337] is characterized in detail for the first time by NMR. Slowly exchanging amides were concentrated in the -sheet region and quasi--helix. The -barrel fold of the cadherin domain is topologically similar to the immunoglobulin fold. Comparison of this solution structure to the crystallized dimers of the N-terminal pair of E-cadherin domains [Nagar et al. (1996) Nature, 380, 360–364] and of the homologous single domain of N-cadherin reveals a conserved cadherin fold with minor structural differences, which can be accounted for by differences in metal ligation and oligomeric state.Abbreviations cad extracellular cadherin repeat - CAM cell adhesion molecule - CSI chemical shift index - DTT dithiothreitol - E-cadherin epithelial cadherin - N-cadherin neural cadherin - NOE nuclear Overhauser enhancement - PFG pulsed field gradient - rmsd root-mean-square deviation     

The relative orientation of the fibronectin 6F11F2 module pair: A 15N NMR relaxation study

The structure of a pair of modules (⁶F1¹F2), that forms part of the collagen-binding region of fibronectin, is refined using heteronuclear relaxation data. A structure of the pair was previously derived from ¹H-¹H NOE and ³ J _HHN data [Bocquier et al. (1999) Structure, 7, 1451–1460] and a weak module–module interface, comprising Leu19 and Leu28, in ⁶F1, and Tyr68 in ²F1, was identified. In this study, the definition of the average relative orientation of the two modules is improved using the dependence of ¹⁵N relaxation on rotational diffusion anisotropy. This structure refinement is based on the selection of a subset of structures from sets calculated with NOE and ³ J _HHN data alone, using the quality of the fits to the relaxation data as the selection criterion. This simple approach is compared to a refinement strategy where ¹⁵N relaxation data are included in the force field as additional restraints [Tjandra et al. (1997) Nat. Struct. Biol., 4, 443–449].     

Fluorescence and circular dichroism spectroscopic studies on bovine lactoperoxidase*

Intrinsic steady-state fluorescence of lactoperoxidase (LPO) and its ligand-bound complexes has been characterized as a structural probe of its structure in solution. On excitation at 295 nm, a broad emission maximum is observed around 338 nm for LPO and for its ligand-bound complexes. The quantum yield is 0.0185±0.0005 for LPO and indicates tryptophan heme energy transfer. Tryptophan residues are located away from heme and are approximately equally distributed among hydrophobic and hydrophilic environments. From Förster resonance energy transfer equations, the average distance between tryptophans and heme within the enzyme is computed to be 25.1±0.2 Å. These fluorescence properties are consistent with the recent theoretical three-dimensional model for LPO and reveal that Trp337 and Trp404 dominate the intrinsic fluorescence, and together contribute 64% of the observed intensity. The effects of the denaturing agents guanidine hydrochloride and urea on the intrinsic fluorescence of LPO and CD of the backbone amide chromophores have been examined. The considerably red shifted emission maximum at 356 nm indicates that tryptophans, buried in the hydrophobic environment, are exposed to the solvent on denaturation. A simple two-state transition between the native and denatured forms of the protein has been used to explain the results. [Denaturant]_1/2 5.5 M, determined from both these experiments, indicates that LPO is relatively stable toward the denaturing agents. Quenching studies using. I^–, Cs⁺ and polar neutral acrylamide are consistent with this picture. Acrylamide can penetrate the protein matrix. It is an efficient quencher and the quenching process is essentially homogeneous with all the tryptophans being accessible. Cs⁺ ion is a very inefficient quencher but the iodide ion shows the quenching process to be predominantly heterogeneous with widely differing tryptophan accessibility. The Stern–Volmer constants deduced are K ^sv =8.4±1.4 M^–1 and K ^sv =4.05±0.65 M_–1 for acrylamide and iodide quenching, respectively. The fractional accessibility, f _a , deduced is f _a =0.52±0.03 for iodide quenching.     

Electrophoretic behavior of the H+-ATPase proteolipid from bovine heart mitochondria

The proteolipid subunit of H⁺-ATPase was labeled by [¹⁴C]N,N-dicyclohexylcarbodiimide in bovine heart mitochondria. The radioactive labeling was followed using various systems of sodium dodecylsulfate polyacrylamide gel electrophoresis (SDS-PAGE). When using discontinuous SDS-PAGE (Laemmli, U.K., 1970,Nature (London)227, 680–685) a monomeric (Mr 7600±1500) and a dimeric form (Mr 17,800±1200) of the proteolipid were detected, while only the monomeric form was found on urea (8 M) containing gels (SDS-PAGE according to Laemmli; or Swank, R. T., and Munkers, K. D., 1971,Anal. Biochem. 39, 462–477). When using SDS-PAGE with Na-P_i buffer (Weber, K., and Osborn, M., 1969,J. Biol. Chem. 244, 4406–4442), only a dimeric form of the proteolipid (Mr 15,000±1000) was detected. Experimental data indicate that the different patterns of proteolipid separation are related to the presence of the two distinct proteolipid conformations in the SDS solution.     

The carboxy-terminal region of human interleukin-5 is essential for maintenance of tertiary structure but not for dimerization

The C-terminal region of interleukin-5 has previously been suggested to be important for biological activity [Mackenzieet al., (1991),Mol. Immunol. 28, 155–158; Kodamaet al. (1991),Biochem. Biophys. Res. Commun. 178, 514–519]. We have investigated this region by making a series of truncation mutants. The proteins were expressed inEscherichia coli, purified from inclusion bodies, and were able to refold with the disulfide homodimeric topology typical of interleukin-5. Analysis of the truncated carboxy-terminal proteins in an interleukin-5-dependent proliferation assay on TF-1 cells showed a rapid loss of activity as the C-terminal was shortened by more than two amino acids. This loss of biological activity correlated with a drop in binding affinity to both the chain of the receptor and the high-affinity complex consisting of the and subunits. Analysis of the proteins by¹H-NMR showed that the truncated mutants have higher exchange rates with solvent, indicating a less rigid structure. The carboxy-terminal region is therefore necessary to maintain the stability of the four-helix bundle and to orient correctly the important residues of the fourth helix. Inspection of the structure determined by X-ray crystallography shows that Trp-110 acts as the major residue in anchoring the fourth helix.     

Refined solution structure of the dimeric N-terminal HHCC domain of HIV-2 integrase

The solution structure of the dimeric N-terminal domain of HIV-2 integrase (residues 1–55, named IN_1–55) has been determined using NMR spectroscopy. The structure of the monomer, which was already reported previously [Eijkelenboom et al. (1997) Curr. Biol., 7, 739–746], consists of four -helices and is well defined. Helices 1, 2 and 3 form a three-helix bundle that is stabilized by zinc binding to His12, His16, Cys40 and Cys43. The dimer interface is formed by the N-terminal tail and the first half of helix 3. The orientation of the two monomeric units with respect to each other shows considerable variation. ¹⁵N relaxation studies have been used to characterize the nature of the intermonomeric disorder. Comparison of the dimer interface with that of the well-defined dimer interface of HIV-1 IN_1–55 shows that the latter is stabilized by additional hydrophobic interactions and a potential salt bridge. Similar interactions cannot be formed in HIV-2 IN_1–55 [Cai et al. (1997) Nat. Struct. Biol., 4, 567–577], where the corresponding residues are positively charged and neutral ones.     

Manifestation of intramolecular motions on pico- and nanosecond time scales in 1H−15N NMR relaxation: Analysis of dynamic models of one- and two-helical subunits of bacterioopsin

Summary The influence of the internal dynamics of two polypeptides comprising transmembrane -helix A or two -helices A and B of bacterioopsin on experimentally accessible ¹⁵N NMR relaxation rates was investigated by molecular dynamics (MD) simulations, combined with more simple mechanic considerations. Model-free order parameters and correlation times of internal motions [Lipari, G. and Szabo, A. (1982) J. Am. Chem. Soc., 104, 4546–4559] were calculated for these models. It was found that both peptides exhibit two types of internal motions of the amide bonds, on the pico- and nanosecond time scales, affecting ¹⁵N NMR relaxation. The fast fluctuations are local and correspond to the librational motions of the individual N–H vectors in an effective potential of atoms of the surrounding matrix. In contrast, the motions on the nanosecond time scale imply concerted collective vibrations of a large number of atoms and could be represented as bending oscillation of -helices, strongly overdamped by the ambient solvent. A few other molecular mechanisms of slow internal motion were found, such as local distortions of the -helices (e.g., -aneurysm), delocalized distortions of the -helical backbone, as well as oscillations of the tilt angle between the axes of the -helices A and B. The results are compared with ¹⁵N NMR relaxation data measured for the (1–36)bacterioopsin and (1–71)bacterioopsin polypeptides in chloroform-methanol (1:1) and in SDS micelles [Orekhov, V.Yu., Pervushin, K.V. and Arseniev, A.S. (1994) Eur. J. Biochem., 219, 887–896].Abbreviations C2 baeterioopsin-(7–63)-peptide - sA bacterioopsin-(7–32)-peptide - CPMG Carr-Purcell-Meiboom-Gill - MD molecular dynamics - rmsd root-mean-square deviation