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Summary7,8-Dihydro-8-oxoguanine (8oxoG) is a major mutagenic base lesion formed when reactive oxygen species react with guanine in DNA. The human 8oxoG DNA glycosylase (hOgg1) recognizes and initiates repair of 8oxoG. hOgg1 is acknowledged as a bifunctional DNA glycosylase catalyzing removal of the damaged base followed by cleavage of the backbone of the intermediate abasic DNA (AP lyase/β-elimination). When acting on 8oxoG-containing DNA, these two steps in the hOgg1 catalysis are considered coupled, with Lys249 implicated as a key residue. However, several lines of evidence point to a concurrent and independent monofunctional hydrolysis of the N-glycosylic bond being the in vivo relevant reaction mode of hOgg1. Here, we present biochemical and structural evidence for the monofunctional mode of hOgg1 by design of separation-of-function mutants. Asp268 is identified as the catalytic residue, while Lys249 appears critical for the specific recognition and final alignment of 8oxoG during the hydrolysis reaction.

Escherichia coli cells with a point mutation in the dnaN gene causing the amino acid change Gly157 to Cys, were found to underinitiate replication and grow with a reduced origin and DNA concentration. The mutant β clamp also caused excessive conversion of ATP-DnaA to ADP-DnaA. The DnaA protein was, however, not the element limiting initiation of replication. Overproduction of DnaA protein, which in wild-type cells leads to over-replication, had no effect in the dnaN(G157C) mutant. Origins already opened by DnaA seemed to remain open for a prolonged period, with a stage of initiation involving β clamp loading, presumably limiting the initiation process. The existence of opened origins led to a moderate SOS response. Lagging strand synthesis, which also requires loading of the β clamp, was apparently unaffected. The result indicates that some aspects of β clamp activity are specific to the origin. It is possible that the origin specific activities of β contribute to regulation of initiation frequency.

Sorting of proteins to Weibel-Palade bodies (WPB) of endothelial cells allows rapid regulated secretion of leukocyte-recruiting P-selectin and chemokines as well as procoagulant von Willebrand factor (VWF). Here we show by domain swap studies that the exposed aspartic acid in loop 2 (Ser(44)-Asp(45)-Gly(46)) of the CXC chemokine interleukin (IL)-8 is crucial for targeting to WPB. Loop 2 also governs sorting of chemokines to alpha-granules of platelets, but the fingerprint of the loop 2 of these chemokines differs from that of IL-8. On the other hand, loop 2 of IL-8 closely resembles a surface-exposed sequence of the VWF propeptide, the region of VWF that directs sorting of the protein to WPB. We conclude that loop 2 of IL-8 constitutes a critical signal for sorting to WPB and propose a general role for this loop in the sorting of chemokines to compartments of regulated secretion.

The human hMYH and NEIL1 genes encode DNA glycosylases involved in repair of oxidative base damage and mutations in these genes are associated with certain cancers. Primary sclerosing cholangitis (PSC), a chronic cholestatic liver disease characterized by inflammatory destruction of the biliary tree, is often complicated by the development of cholangiocarcinoma (CCA). Here, we aimed to investigate the influence of genetic variations in the hMYH and NEIL1 genes on risk of CCA in PSC patients. The hMYH and NEIL1 gene loci in addition to the DNA repair genes hOGG1, NTHL1 and NUDT1 were analyzed in 66 PSC patients (37 with CCA and 29 without cancer) by complete genomic sequencing of exons and adjacent intronic regions. Several single-nucleotide polymorphisms and mutations were identified and severe impairment of protein function was observed for three non-synonymous variants. The NEIL1 G83D mutant was dysfunctional for the major oxidation products 7,8-dihydro-8-oxoguanine (8oxoG), thymine glycol and dihydrothymine in duplex DNA, and the ability to perform delta-elimination at abasic sites was significantly reduced. The hMYH R260Q mutant had severe defect in adenine DNA glycosylase activity, whereas hMYH H434D could excise adenines from A:8oxoG pairs but not from A:G mispairs. We found no overall associations between the 18 identified variants and susceptibility to CCA in PSC patients; however, the impaired variants may be of significance for carcinogenesis in general. Our findings demonstrate the importance of complete resequencing of selected candidate genes in order to identify rare genetic variants and their possible contribution to individual susceptibility to cancer development.

3-methyladenine DNA glycosylases initiate repair of cytotoxic and promutagenic alkylated bases in DNA. We demonstrate by comparative modelling that Bacillus cereus AlkD belongs to a new, fifth, structural superfamily of DNA glycosylases with an alpha-alpha superhelix fold comprising six HEAT-like repeats. The structure reveals a wide, positively charged groove, including a putative base recognition pocket. This groove appears to be suitable for the accommodation of double-stranded DNA with a flipped-out alkylated base. Site-specific mutagenesis within the recognition pocket identified several residues essential for enzyme activity. The results suggest that the aromatic side chain of a tryptophan residue recognizes electron-deficient alkylated bases through stacking interactions, while an interacting aspartate-arginine pair is essential for removal of the damaged base. A structural model of AlkD bound to DNA with a flipped-out purine moiety gives insight into the catalytic machinery for this new class of DNA glycosylases.

The sodium (Na(+))-calcium (Ca(2+)) exchanger 1 (NCX1) is an important regulator of intracellular Ca(2+) homeostasis. Serine 68-phosphorylated phospholemman (pSer-68-PLM) inhibits NCX1 activity. In the context of Na(+)/K(+)-ATPase (NKA) regulation, pSer-68-PLM is dephosphorylated by protein phosphatase 1 (PP1). PP1 also associates with NCX1; however, the molecular basis of this association is unknown. In this study, we aimed to analyze the mechanisms of PP1 targeting to the NCX1-pSer-68-PLM complex and hypothesized that a direct and functional NCX1-PP1 interaction is a prerequisite for pSer-68-PLM dephosphorylation. Using a variety of molecular techniques, we show that PP1 catalytic subunit (PP1c) co-localized, co-fractionated, and co-immunoprecipitated with NCX1 in rat cardiomyocytes, left ventricle lysates, and HEK293 cells. Bioinformatic analysis, immunoprecipitations, mutagenesis, pulldown experiments, and peptide arrays constrained PP1c anchoring to the K(I/V)FF motif in the first Ca(2+) binding domain (CBD) 1 in NCX1. This binding site is also partially in agreement with the extended PP1-binding motif K(V/I)FF-X5-8Φ1Φ2-X8-9-R. The cytosolic loop of NCX1, containing the K(I/V)FF motif, had no effect on PP1 activity in an in vitro assay. Dephosphorylation of pSer-68-PLM in HEK293 cells was not observed when NCX1 was absent, when the K(I/V)FF motif was mutated, or when the PLM- and PP1c-binding sites were separated (mimicking calpain cleavage of NCX1). Co-expression of PLM and NCX1 inhibited NCX1 current (both modes). Moreover, co-expression of PLM with NCX1(F407P) (mutated K(I/V)FF motif) resulted in the current being completely abolished. In conclusion, NCX1 is a substrate-specifying PP1c regulator protein, indirectly regulating NCX1 activity through pSer-68-PLM dephosphorylation.

Introduction: The cardiac Na+/Ca2+ exchanger 1 (NCX1) modulates excitation-contraction coupling and contributes to Ca2+ removal in cardiomyocytes. Altered expression and activity of NCX1 is linked to dysfunctional Ca2+ handling in chronic heart disease. Consequently, modulation of NCX1 activity is proposed as a therapeutic target. The cytosolic loop of NCX1, ∼550 amino acids, comprises several important docking and regulation sites. In particular, phospholemman (PLM) has been shown to interact and inhibit NCX1 activity when phosphorylated at serine 68 (pSer68-PLM). Importantly, pSer68-PLM has been shown as a substrate for protein phosphatase 1 (PP1) in the context of PLM regulation of the sodium-potassium pump. PP1 regulation of NCX1 is unknown.Hypothesis: PP1 binds to NCX1 and regulates its activity by dephosphorylating pSer68-PLM.Methods and Results: Using co-immunoprecipitation in rat heart lysates we have shown that NCX1 exists in a macromolecular complex with PP1 and PLM. This facilitates specific control of NCX function. Bioinformatic analysis revealed three putative PP1 binding sites on NCX1. Co-localization studies, co-immunoprecipitations, pull down, mutation- and peptide overlay assays indicated that PP1 bound directly to the consensus sequence R/KVxF in calcium binding domain 1 (CBD1) of NCX1. The reciprocal NCX1 binding site in PP1 was identified within residues 235-260, a region which harbours important anchoring sites. A peptide docking model was generated showing how the R/KVxF peptide may bind in the hydrophobic pocket of PP1. Surface plasmon resonance analysis indicated that the NCX1-PP1 binding is strong and stable. This binding does not inhibit PP1 activity. Co-expression of NCX1 with PLM and PP1 in HEK293 down regulates pSer68-PLM, indicating that PP1-R/KVxF- binding is a prerequisite for dephosphorylation of pSer68-PLM.Conclusion: R/KVxF motif in NCX1-CBD1 anchors PP1, does not change the activity of the enzyme and facilitates dephosphorylation of pSer68-PLM.

We describe the cloning, overexpression, purification, characterization and crystal structure of chitinase G, a single-domain family 19 chitinase from the Gram-positive bacterium Streptomyces coelicolor A3(2). Although chitinase G was not capable of releasing 4-methylumbelliferyl from artificial chitooligosaccharide substrates, it was capable of degrading longer chitooligosaccharides at rates similar to those observed for other chitinases. The enzyme was also capable of degrading a colored colloidal chitin substrate (carboxymethyl-chitin-remazol-brilliant violet) and a small, presumably amorphous, subfraction of alpha-chitin and beta-chitin, but was not capable of degrading crystalline chitin completely. The crystal structures of chitinase G and a related Streptomyces chitinase, chitinase C [Kezuka Y, Ohishi M, Itoh Y, Watanabe J, Mitsutomi M, Watanabe T & Nonaka T (2006) J Mol Biol358, 472-484], showed that these bacterial family 19 chitinases lack several loops that extend the substrate-binding grooves in family 19 chitinases from plants. In accordance with these structural features, detailed analysis of the degradation of chitooligosaccharides by chitinase G showed that the enzyme has only four subsites (- 2 to + 2), as opposed to six (- 3 to + 3) for plant enzymes. The most prominent structural difference leading to reduced size of the substrate-binding groove is the deletion of a 13-residue loop between the two putatively catalytic glutamates. The importance of these two residues for catalysis was confirmed by a site-directed mutagenesis study.

Many Gram-positive bacteria produce ribosomally synthesized antimicrobial peptides, often termed bacteriocins. Genes encoding pediocin-like bacteriocins are generally cotranscribed with or in close vicinity to a gene encoding a cognate immunity protein that protects the bacteriocin-producer from their own bacteriocin. We present the first crystal structure of a pediocin-like immunity protein, EntA-im, conferring immunity to the bacteriocin enterocin A. Determination of the structure of this 103-amino acid protein revealed that it folds into an antiparallel four-helix bundle with a flexible C-terminal part. The fact that the immunity protein conferring immunity to carnobacteriocin B2 also consists of a four-helix bundle (Sprules, T., Kawulka, K. E., and Vederas, J. C. (2004) Biochemistry 43, 11740-11749) strongly indicates that this is a conserved structural motif in all pediocin-like immunity proteins. The C-terminal half of the immunity protein contains a region that recognizes the C-terminal half of the cognate bacteriocin, and the flexibility in the C-terminal end of the immunity protein might thus be an important characteristic that enables the immunity protein to interact with its cognate bacteriocin. By homology modeling of three other pediocin-like immunity proteins and calculation of the surface charge distribution for EntA-im and the three structure models, different charge distributions were observed. The differences in the latter part of helix 3, the beginning of helix 4, and the loop connecting these helices might also be of importance in determining the specificity.

Pediocin-like antimicrobial peptides (AMPs) form a group of lactic acid bacteria produced, cationic membrane-permeabilizing peptides with 37 to 48 residues. Upon exposure to membrane-mimicking entities, their hydrophilic, cationic, and highly conserved N-terminal region forms a three-stranded antiparallel β-sheet supported by a conserved disulfide bridge. This N-terminal β-sheet region is followed by a central amphiphilic α-helix and this in most (if not all) of these peptides is followed by a rather extended C-terminal tail that folds back onto the central α-helix, thereby creating a hairpin-like structure in the C-terminal half. There is a flexible hinge between the β-sheet N-terminal region and the hairpin C-terminal region and one thus obtains two domains that may move relative to each other. The cationic N-terminal β-sheet domain mediates binding of the pediocin-like AMPs to the target-cell surface through electrostatic interactions, while the more hydrophobic and amphiphilic C-terminal hairpin domain penetrates into the hydrophobic part of the target-cell membrane, thereby mediating leakage through the membrane. The hinge provides the structural flexibility that enables the C-terminal hairpin domain to dip into the hydrophobic part of the membrane. Despite extensive sequence similarities, these AMPs differ markedly in their target-cell specificity, and results obtained with hybrid AMPs indicate that the membrane-penetrating hairpin-like C-terminal domain is the major specificity determinant. Bacteria that produce pediocin-like AMPs also produce a 11-kDa cognate immunity protein that protects the producer. The immunity proteins are well-structured, 4-helix bundle cytosolic proteins. They show a high degree of specificity in that they largely recognize and confer immunity only to their cognate AMP and in some cases to a few AMPs that are closely related to their cognate AMP. The C-terminal half of the immunity proteins contains a domain that is involved in specific recognition of the C-terminal membrane-penetrating specificity-determining hairpin domain of the cognate AMP. Copyright © 2005 European Peptide Society and John Wiley & Sons, Ltd.

The stability of tetrameric malate dehydrogenase from the green phototrophic bacterium Chloroflexus aurantiacus (CaMDH) is at least in part determined by electrostatic interactions at the dimer-dimer interface. Since previous studies had indicated that the thermal stability of CaMDH becomes lower with increasing pH, attempts were made to increase the stability by removal of (excess) negative charge at the dimer-dimer interface. Mutation of Glu165 to Gln or Lys yielded a dramatic increase in thermal stability at pH 7.5 (+23.6 -- + 23.9 degrees C increase in apparent t(m)) and a more moderate increase at pH 4.4 (+4.6 -- + 5.4 degrees C). The drastically increased stability at neutral pH was achieved without forfeiture of catalytic performance at low temperatures. The crystal structures of the two mutants showed only minor structural changes close to the mutated residues, and indicated that the observed stability effects are solely due to subtle changes in the complex network of electrostatic interactions in the dimer-dimer interface. Both mutations reduced the concentration dependency of thermal stability, suggesting that the oligomeric structure had been reinforced. Interestingly, the two mutations had similar effects on stability, despite the charge difference between the introduced side-chains. Together with the loss of concentration dependency, this may indicate that both E165Q and E165K stabilize CaMDH to such an extent that disruption of the inter-dimer electrostatic network around residue 165 no longer limits kinetic thermal stability.

The crystal structures of mixtures of d - and l -enantiomers of hydrophobic amino acids, either as true racemates or 1:1 complexes between two different acids, are always divided into hydrophilic and hydrophobic layers. Two different aggregation patterns are observed, each with a unique hydrogen bonding arrangement. In an attempt to find which pattern is inherently the most favourable, ab initio calculations on two-dimensional slabs of the hydrophilic regions in these crystals have been carried out. The results clearly show that one hydrogen bonding pattern has a higher interaction energy.

Malate dehydrogenase (MDH) from the moderately thermophilic bacterium Chloroflexus aurantiacus (CaMDH) is a tetrameric enzyme, while MDHs from mesophilic organisms usually are dimers. To investigate the potential contribution of the extra dimer-dimer interface in CaMDH with respect to thermal stability, we have engineered an intersubunit disulfide bridge designed to strengthen dimer-dimer interactions. The resulting mutant (T187C, containing two 187-187 disulfide bridges in the tetramer) showed a 200-fold increase in half-life at 75 degrees C and an increase of 15 deg. C in apparent melting temperature compared to the wild-type. The crystal structure of the mutant (solved at 1.75 A resolution) was essentially identical with that of the wild-type, with the exception of the added inter-dimer disulfide bridge and the loss of an aromatic intra-dimer contact. Remarkably, the mutant and the wild-type had similar temperature optima and activities at their temperature optima, thus providing a clear case of uncoupling of thermal stability and thermoactivity. The results show that tetramerization may contribute to MDH stability to an extent that depends strongly on the number of stabilizing interactions in the dimer-dimer interface.

Free P(OCH3)3 has been studied by gas electron diffraction (GED) and DFT calculations at the B3PW91/6-311+G* level. Each conformer is characterised by three dihedral angles τ(COPlp) where lp denotes the direction of the electron lone pair on the P atom; assumed to lie in a plane containing the P–O bond and bisecting the opposing OPO angle. DFT calculations indicate that the most stable conformer is an anti,gauche+,gauche+ (ag+g+) conformer characterised by the angles τa = (COPlp) −173, τb = 54 and τc = 41°. It is followed by an ag−g+ conformer at ΔE = 6.3 kJ mol−1, an aa+g+ conformer at ΔE = 6.6 kJ mol−1, and a g+g+g+ conformer at ΔE = 10.4 kJ mol−1. The calculated standard free energies at 298.15 K indicate that the mole fractions in the gas phase at this temperature are χ(±ag+g+) = 73%, χ(ag−g+) = 16%, χ(±aa+g+) = 10% and χ(±ag+g+g+) =1%; GED data indicate that the mole fractions of the more stable conformers at room temperature are χ(±ag+g+) = 78(13)%, χ(ag−g+) = 9(11)% and χ(±aa+g+) = 14(21)%. Natural Bond Orbital (NBO) analysis of the wavefunctions suggest that while bond distances and valence angles are determined by anomeric effects, the relative stabilities of the four conformers are not determined by such effects alone. Examination of the crystal structures of 287 complexes where one or more P(OCH3)3 units are coordinated to a d-block transition metal M, shows that in the 523 crystallographically independent MP(OCH3)3 fragments 46% of the trimethylphosphite units adopt a ±ag+g+ conformation, 19% an ag−g+ conformation and 30% a ±aa+g+ conformation. It is suggested that the increased number of ±aa+g+ conformers and decreased number of ±ag+g+ conformers relative to the gas phase, as well as the folding back of the gauche ligands are due to interligand repulsion in the transition metal complexes. Structure optimisation of F2POMe by DFT calculations at the B3PW91/6-311+G* level indicate that the most stable conformation is anti, while the energy of a gauche conformer is about 15 kJ mol−1 higher. NBO analysis of the wavefunctions indicate that the relative stabilities of the two conformers as well as the differences between bond distances and valence angles may be determined by anomeric effects.

Deamination of the exocyclic amines in adenine, guanine and cytosine forms base lesions that may lead to mutations if not removed by DNA repair proteins. Prokaryotic endonuclease V (EndoV/Nfi) has long been known to incise DNA 3′ to a variety of base lesions, including deaminated adenine, guanine and cytosine. Biochemical and genetic data implicate that EndoV is involved in repair of these deaminated bases. In contrast to DNA glycosylases that remove a series of modified/damaged bases in DNA by direct excision of the nucleobase, EndoV cleaves the DNA sugar phosphate backbone at the second phosphodiester 3′ to the lesion without removing the deaminated base. Structural investigation of this unusual incision by EndoV has unravelled an enzyme with separate base lesion and active site pockets. A novel wedge motif was identified as a DNA strand-separation feature important for damage detection. Human EndoV appears inactive on DNA, but has been shown to incise various RNA substrates containing inosine. Inosine is the deamination product of adenosine and is frequently found in RNA. The structural basis for discrimination between DNA and RNA by human EndoV remains elusive.

Cardiac sodium (Na(+))-calcium (Ca(2+)) exchanger 1 (NCX1) is central to the maintenance of normal Ca(2+) homeostasis and contraction. Studies indicate that the Ca(2+)-activated protease calpain cleaves NCX1. We hypothesized that calpain is an important regulator of NCX1 in response to pressure overload and aimed to identify molecular mechanisms and functional consequences of calpain binding and cleavage of NCX1 in the heart. NCX1 full-length protein and a 75-kDa NCX1 fragment along with calpain were up-regulated in aortic stenosis patients and rats with heart failure. Patients with coronary artery disease and sham-operated rats were used as controls. Calpain co-localized, co-fractionated, and co-immunoprecipitated with NCX1 in rat cardiomyocytes and left ventricle lysate. Immunoprecipitations, pull-down experiments, and extensive use of peptide arrays indicated that calpain domain III anchored to the first Ca(2+) binding domain in NCX1, whereas the calpain catalytic region bound to the catenin-like domain in NCX1. The use of bioinformatics, mutational analyses, a substrate competitor peptide, and a specific NCX1-Met(369) antibody identified a novel calpain cleavage site at Met(369). Engineering NCX1-Met(369) into a tobacco etch virus protease cleavage site revealed that specific cleavage at Met(369) inhibited NCX1 activity (both forward and reverse mode). Finally, a short peptide fragment containing the NCX1-Met(369) cleavage site was modeled into the narrow active cleft of human calpain. Inhibition of NCX1 activity, such as we have observed here following calpain-induced NCX1 cleavage, might be beneficial in pathophysiological conditions where increased NCX1 activity contributes to cardiac dysfunction.

Deamination of the nucleobases in DNA and RNA is a result of spontaneous hydrolysis, endogenous or environmental factors as well as deaminase enzymes. Adenosine is deaminated to inosine which is miscoding and preferentially base pairs with cytosine. In the case of DNA, this is a premutagenic event that is counteracted by DNA repair enzymes specifically engaged in recognition and removal of inosine. However, in RNA, inosine is an essential modification introduced by specialized enzymes in a highly regulated manner to generate transcriptome diversity. Defect editing is seen in various human disease including cancer, viral infections and neurological and psychiatric disorders. Enzymes catalyzing the deaminase reaction are well characterized and recently an unexpected function of Endonuclease V in RNA processing was revealed. Whereas bacterial Endonuclease V enzymes are classified as DNA repair enzymes, it appears that the mammalian enzymes are involved in processing of inosine in RNA. This yields an interesting yet unexplored, link between DNA and RNA processing. Further work is needed to gain understanding of the impact of inosine in DNA and RNA under normal physiology and disease progression.

Albumin is the most abundant protein in blood and plays a pivotal role as a multitransporter of a wide range of molecules such as fatty acids, metabolites, hormones, and toxins. In addition, it binds a variety of drugs. Its role as distributor is supported by its extraordinary serum half-life of 3 weeks. This is related to its size and binding to the cellular receptor FcRn, which rescues albumin from intracellular degradation. Furthermore, the long half-life has fostered a great and increasing interest in utilization of albumin as a carrier of protein therapeutics and chemical drugs. However, to fully understand how FcRn acts as a regulator of albumin homeostasis and to take advantage of the FcRn-albumin interaction in drug design, the interaction interface needs to be dissected. Here, we used a panel of monoclonal antibodies directed towards human FcRn in combination with site-directed mutagenesis and structural modeling to unmask the binding sites for albumin blocking antibodies and albumin on the receptor, which revealed that the interaction is not only strictly pH-dependent, but predominantly hydrophobic in nature. Specifically, we provide mechanistic evidence for a crucial role of a cluster of conserved tryptophan residues that expose a pH-sensitive loop of FcRn, and identify structural differences in proximity to these hot spot residues that explain divergent cross-species binding properties of FcRn. Our findings expand our knowledge of how FcRn is controlling albumin homeostasis at a molecular level, which will guide design and engineering of novel albumin variants with altered transport properties. This research was originally published in: Journal of Biological Chemistry. © the American Society for Biochemistry and Molecular Biology.

A major challenge for the therapeutic use of many peptides and proteins is their short circulatory half-life. Albumin has an extended serum half-life of 3 weeks because of its size and FcRn-mediated recycling that prevents intracellular degradation, properties shared with IgG antibodies. Engineering the strictly pH-dependent IgG-FcRn interaction is known to extend IgG half-life. However, this principle has not been extensively explored for albumin. We have engineered human albumin by introducing single point mutations in the C-terminal end that generated a panel of variants with greatly improved affinities for FcRn. One variant (K573P) with 12-fold improved affinity showed extended serum half-life in normal mice, mice transgenic for human FcRn, and cynomolgus monkeys. Importantly, favorable binding to FcRn was maintained when a single-chain fragment variable antibody was genetically fused to either the N- or the C-terminal end. The engineered albumin variants may be attractive for improving the serum half-life of biopharmaceuticals. This research was originally published in: Journal of Biological Chemistry. © the American Society for Biochemistry and Molecular Biology.

6-Substituted purin-2-ones have been prepared by completely regioselective addition of Grignard reagents to an N-protected purin-2-one followed by rearomatisation and deprotection. The target compounds may be regarded as analogues of the potent cytokinins trans-zeatin and benzylaminopurine (BAP), and most of the BAP analogues did induce increased weight growth in radish cotyledons. N-Protected (E)-6-styrylpurin-2-one underwent head to tail [2+2] dimerisation to the 1α,2α,3β,4β-substituted cyclobutane 15, when exposed to ordinary daylight. When irradiated with UV-light, the trans-compound isomerised to the corresponding cis-isomer. The structure of compound 15 was determined by single crystal X-ray diffraction methods at 150 K.

A reinvestigation of the crystal structure of the 1:1 mixture of the two racemates DL-isoleucine and DL-allo-isoleucine, with a detailed analysis of interatomic distances between alternative side-chain positions, reveals a systematic distribution of the four stereoisomers in this crystal. Two different molecular chains exist in the crystal and each such chain accommodates a single diastereomeric pair only (L-isoleucine:D-allo-isoleucine or D-isoleucine:L-allo-isoleucine). The crystal is built up by a stacking of such chains in two dimensions and three different packing modes for the two types of chains are discussed. Crystallization experiments of the two individual racemates in the 1:1 mixture of DL-isoleucine:DL-allo-isoleucine have been undertaken. The structure of the racemate DL-isoleucine is presented. The molecular arrangements in this racemate and the 1:1 DL-isoleucine:DL-allo-isoleucine mixture are closely related. Furthermore, the spontaneous resolution of enantiomers upon crystallization of the other racemate, DL-allo-isoleucine, is rationalized on the basis of the aforementioned analysis of interatomic distances in the 1:1 DL-isoleucine:DL-allo-isoleucine complex. Structural data for a new L-isoleucine: D-allo-isoleucine complex are also given.

DL-Allylglycine (DL-2-amino-4-pentenoic acid, C5H9NO2) yields crystals with Pca21 symmetry and two crystallographically independent yet pseudo-inversion-related enantiomers. The distribution among the common space groups of other crystalline racemates with more than one molecule in the asymmetric unit has been established. The conformational similarities between crystallographically independent enantiomers in 114 non-centrosymmetric racemates were quantified using the r.m.s. deviation for a molecular superposition. The analysis shows that in the majority of crystals the conformations of the crystallographically independent molecules are very similar with mean r.m.s. deviation = 0.190 Å. In almost 80% of the structures the mean r.m.s. deviations is in the interval 0–0.2 Å. It is estimated that racemates constitute 23% of the centrosymmetric organic structures in the Cambridge Structural Database.

The amino acid L-isoleucine has been cocrystallized with seven selected D-amino acids including D-methionine [L-isoleucine–D-methionine (1/1), C6H13NO2.C5H11NO2S, amino-acid side chain R = —CH2—CH2—S—CH3] and a homologous series from D-alanine [L-isoleucine–D-alanine (1/1), C6H13NO2.C3H7NO2, R = —CH3] through D-α-aminobutyric acid [L-isoleucine–D-α-aminobutyric acid (1/1), C6H13NO2.C4H9NO2, R = —CH2—CH3] and D-norvaline [L-isoleucine–D-norvaline (1/1), C6H13NO2.C5H11NO2, R = —CH2—CH2—CH3] to D-norleucine [L-isoleucine–D-norleucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH2—CH2—CH3] with linear side chains, and D-valine [L-isoleucine–D-valine (1/1), C6H13NO2.C5H11NO2, R = —CH—(CH3)2] and D-leucine [L-isoleucine–D-leucine (1/1), C6H13NO2.C6H13NO2, R = —CH2—CH—(CH3)2] with branched side chains. All the crystal structures are divided into distinct hydrophilic and hydrophobic layers. In the five complexes with amino acids with linear side chains the polar parts of the D- and L-amino acids are related by pseudo-glide-plane symmetry, and four of them have remarkably similar molecular arrangements. The D-valine and D-leucine complexes, on the other hand, are structurally quite different with the polar parts of the D- and L-amino acids related by pseudo-inversion. Differences in the hydrogen-bond pattern in the two molecular arrangements are discussed.

Endonuclease V orthologues are highly conserved proteins found in all kingdoms of life. While the prokaryotic enzymes are DNA repair proteins for removal of deaminated adenosine (inosine) from the genome, no clear role for the eukaryotic counterparts has hitherto been described. Here we report that human endonuclease V (ENDOV) and also Escherichia coli endonuclease V are highly active ribonucleases specific for inosine in RNA. Inosines are normal residues in certain RNAs introduced by specific deaminases. Adenosine-to-inosine editing is essential for proper function of these transcripts and defects are linked to various human disease. Here we show that human ENDOV cleaves an RNA substrate containing inosine in a position corresponding to a biologically important site for deamination in the Gabra-3 transcript of the GABAA neurotransmitter. Further, human ENDOV specifically incises transfer RNAs with inosine in the wobble position. This previously unknown RNA incision activity may suggest a role for endonuclease V in normal RNA metabolism., Bacterial endonuclease V enzymes are characterized as DNA repair proteins. Here the authors show that human endonuclease V is an inosine-specific ribonuclease, indicating a role for this enzyme in normal RNA metabolism rather than DNA repair.

8-Oxoguanine DNA glycosylase (OGG) activity was measured by an in vitro assay in lymphocytes of healthy volunteers genotyped for various OGG1 polymorphisms. Only homozygous carriers of the polymorphic C326 allele showed a significantly lower OGG activity compared to the homozygous S326 genotype. The purified S326C OGG1 showed a decreased ability to complete the repair synthesis step in a base excision repair reaction reconstituted in vitro. The propensity of this variant to dimerize as well as its catalytic impairment were shown to be enhanced under oxidizing conditions. Mass spectrometry revealed that the extra cysteine of the variant protein is involved in disulfide bonds compatible with significant conformational changes and/or dimerization. We propose that the S326C OGG1 catalytic impairment and its susceptibility to dimerization and disulfide bond formation in an oxidizing environment all concur to decrease repair capacity. Consequently, the C326 homozygous carriers may be at increased risk of oxidative pathologies.

The functions of several SOS regulated genes in Escherichia coli are still unknown, including dinQ. In this work we characterize dinQ and two small RNAs, agrA and agrB, with antisense complementarity to dinQ. Northern analysis revealed five dinQ transcripts, but only one transcript (+44) is actively translated. The +44 dinQ transcript translates into a toxic single transmembrane peptide localized in the inner membrane. AgrB regulates dinQ RNA by RNA interference to counteract DinQ toxicity. Thus the dinQ-agr locus shows the classical features of a type I TA system and has many similarities to the tisB-istR locus. DinQ overexpression depolarizes the cell membrane and decreases the intracellular ATP concentration, demonstrating that DinQ can modulate membrane-dependent processes. Augmented DinQ strongly inhibits marker transfer by Hfr conjugation, indicating a role in recombination. Furthermore, DinQ affects transformation of nucleoid morphology in response to UV damage. We hypothesize that DinQ is a transmembrane peptide that modulates membrane-dependent activities such as nucleoid compaction and recombination., Author Summary Exposure of the bacterium Escherichia coli to DNA damaging agents induces the SOS response, which up-regulates gene functions involved in numerous cellular processes such as DNA repair, cell division, and replication. Most of the SOS regulated genes in E. coli have been characterized, but still there are several genes of unknown function. One of these uncharacterized genes is dinQ. In this work we characterize dinQ and two novel small RNAs, agrA and agrB, that regulate expression of dinQ. The DinQ peptide is localized in the inner membrane as a single transmembrane peptide of 27 amino acids. Small proteins of less than 50 amino acids are important in cellular processes such as regulation, signalling, and antibacterial action. Here we demonstrate that DinQ modulates recombination and transformation of nucleoid morphology in response to UV damage. Our results provide new insights into small hydrophobic peptides that could regulate important DNA metabolic processes dependent on the inner membrane of the cell.

The asymmetric unit (CI7H25N3Os.C3H80.2H20) con- sists of two crystallographically independent peptide molecules, A and B, with different conformations, X~ being trans and gauche- for the Leu residues in mol- ecules A and B, respectively. The backbone conforma- tion of both peptide molecules resembles that of the /3-pleated sheet arrangement found in proteins. Compar- ison with two other structures containing the tripeptide Gly-L-Leu-L-Tyr reveals almost identical molecular con- formations, and in one instance also a common packing pattern. References Cremer, D. & Pople, J. A. (1975). J. Am. Chem. Soc. 97, 1354-1358. Crevisy, S., Couturier, M., Dugave, C., Dory, Y. L. & Deslongchamps, P. (1995). Bull. Chim. Soc. Fr. 132, 360-371. Deslongchamps, P. (1991). Aldrichimica Acta, 24, 43-56. Drouin, M., Lamothe, S. & Michel, A. (1992). Acta Cryst. C48, 2151- 2154. Gabe, E. J., Le Page, Y., Charland, J.-P., Lee, F. L. & White, P. S. (1989).

The crystal structure of the title compound, C7H14N2O4, contains an intramolecular hydrogen bond between the side-chain hydroxyl group and the main-chain carboxyl­ate group. This is the first observation of such an interaction for a C-terminal l-Ser or l-Thr residue.

Loss of amino groups from adenines in DNA results in the formation of hypoxanthine (Hx) bases with miscoding properties. The primary enzyme in Escherichia coli for DNA repair initiation at deaminated adenine is endonuclease V (endoV), encoded by the nfi gene, which cleaves the second phosphodiester bond 3′ of an Hx lesion. Endonuclease V orthologs are widespread in nature and belong to a family of highly conserved proteins. Whereas prokaryotic endoV enzymes are well characterized, the function of the eukaryotic homologs remains obscure. Here we describe the human endoV ortholog and show with bioinformatics and experimental analysis that a large number of transcript variants exist for the human endonuclease V gene (ENDOV), many of which are unlikely to be translated into functional protein. Full-length ENDOV is encoded by 8 evolutionary conserved exons covering the core region of the enzyme, in addition to one or more 3′-exons encoding an unstructured and poorly conserved C-terminus. In contrast to the E. coli enzyme, we find recombinant ENDOV neither to incise nor bind Hx-containing DNA. While both enzymes have strong affinity for several branched DNA substrates, cleavage is observed only with E. coli endoV. We find that ENDOV is localized in the cytoplasm and nucleoli of human cells. As nucleoli harbor the rRNA genes, this may suggest a role for the protein in rRNA gene transactions such as DNA replication or RNA transcription.

Albumin is the most abundant protein in blood where it has a pivotal role as a transporter of fatty acids and drugs. Like IgG, albumin has long serum half-life, protected from degradation by pH-dependent recycling mediated by interaction with the neonatal Fc receptor, FcRn. Although the FcRn interaction with IgG is well characterized at the atomic level, its interaction with albumin is not. Here we present structure-based modelling of the FcRn–albumin complex, supported by binding analysis of site-specific mutants, providing mechanistic evidence for the presence of pH-sensitive ionic networks at the interaction interface. These networks involve conserved histidines in both FcRn and albumin domain III. Histidines also contribute to intramolecular interactions that stabilize the otherwise flexible loops at both the interacting surfaces. Molecular details of the FcRn–albumin complex may guide the development of novel albumin variants with altered serum half-life as carriers of drugs., Albumin transport proteins circulate in the blood and are protected from degradation by interaction with the neonatal Fc receptor. Andersen et al. investigate the albumin binding site of the neonatal Fc receptor and find pH sensitive ionic networks at the binding interface.

Escherichia coli cells with a point mutation in the dnaN gene causing the amino acid change Gly157 to Cys, were found to underinitiate replication and grow with a reduced origin and DNA concentration. The mutant β clamp also caused excessive conversion of ATP-DnaA to ADP-DnaA. The DnaA protein was, however, not the element limiting initiation of replication. Overproduction of DnaA protein, which in wild-type cells leads to over-replication, had no effect in the dnaN(G157C) mutant. Origins already opened by DnaA seemed to remain open for a prolonged period, with a stage of initiation involving β clamp loading, presumably limiting the initiation process. The existence of opened origins led to a moderate SOS response. Lagging strand synthesis, which also requires loading of the β clamp, was apparently unaffected. The result indicates that some aspects of β clamp activity are specific to the origin. It is possible that the origin specific activities of β contribute to regulation of initiation frequency.

The ada operon of Mycobacterium tuberculosis, which encodes a composite protein of AdaA and AlkA and a separate AdaB/Ogt protein, was characterized. M. tuberculosis treated with N-methyl-N'-nitro-N-nitrosoguanidine induced transcription of the adaA-alkA and adaB genes, suggesting that M. tuberculosis mount an inducible response to methylating agents. Survival assays of the methyltransferase defective Escherichia coli mutant KT233 (ada ogt), showed that expression of the adaB gene rescued the alkylation sensitivity. Further, adaB but not adaA-alkA complemented the hypermutator phenotype of KT233. Purified AdaA-AlkA and AdaB possessed methyltransferase activity. These data suggested that AdaB counteract the cytotoxic and mutagenic effect of O(6)-methylguanine, while AdaA-AlkA most likely transfers methyl groups from innocuous methylphosphotriesters. AdaA-AlkA did not possess alkylbase DNA glycosylase activity nor rescue the alkylation sensitivity of the E. coli mutant BK2118 (tag alkA). We propose that AdaA-AlkA is a positive regulator of the adaptive response in M. tuberculosis. It thus appears that the ada operon of M. tuberculosis suppresses the mutagenic effect of alkylation but not the cytotoxic effect of lesions such as 3-methylpurines. Collectively, these data indicate that M. tuberculosis hypermutator strains with defective adaptive response genes might sustain robustness to cytotoxic alkylation DNA damage and confer a selective advantage contributing to host adaptation.

6-Substituted purin-2-ones have been prepared by completely regioselective addition of Grignard reagents to an N-protected purin-2-one followed by rearomatisation and deprotection. The target compounds may be regarded as analogues of the potent cytokinins trans-zeatin and benzylaminopurine (BAP), and most of the BAP analogues did induce increased weight growth in radish cotyledons. N-Protected (E)-6-styrylpurin-2-one underwent head to tail [2+2] dimerisation to the 1α,2α,3β,4β-substituted cyclobutane 15, when exposed to ordinary daylight. When irradiated with UV-light, the trans-compound isomerised to the corresponding cis-isomer. The structure of compound 15 was determined by single crystal X-ray diffraction methods at 150 K.

Endogenous DNA damage induced by hydrolysis, reactive oxygen species and alkylation modifies DNA bases and the structure of the DNA duplex. Numerous mechanisms have evolved to protect cells from these deleterious effects. Base excision repair is the major pathway for removing base lesions. However, several mechanisms of direct base damage reversal, involving enzymes such as transferases, photolyases and oxidative demethylases, are specialized to remove certain types of photoproducts and alkylated bases. Mismatch excision repair corrects for misincorporation of bases by replicative DNA polymerases. The determination of the 3D structure and visualization of DNA repair proteins and their interactions with damaged DNA have considerably aided our understanding of the molecular basis for DNA base lesion repair and genome stability. Here, we review the structural biochemistry of base lesion recognition and initiation of one-step direct reversal (DR) of damage as well as the multistep pathways of base excision repair (BER), nucleotide incision repair (NIR) and mismatch repair (MMR).

Endonuclease V can initiate the repair of deaminated purine bases by recognizing them and hydrolyzing the second phosphodiester bond on their 3′ side. Now the crystal structures of endonuclease V in complex with its substrate and its product reveal a wedge motif acting as a minor groove–damage sensor and a pocket to recognize the lesion; the enzyme remains tightly bound to the 5′ phosphate product, perhaps to hand it over to downstream repair factors. Endonuclease V (EndoV) initiates a major base-repair pathway for nitrosative deamination resulting from endogenous processes and increased by oxidative stress from mitochondrial dysfunction or inflammatory responses. We solved the crystal structures of Thermotoga maritima EndoV in complex with a hypoxanthine lesion substrate and with product DNA. The PYIP wedge motif acts as a minor groove–damage sensor for helical distortions and base mismatches and separates DNA strands at the lesion. EndoV incises DNA with an unusual offset nick 1 nucleotide 3′ of the lesion, as the deaminated adenine is rotated ∼90° into a recognition pocket ∼8 A from the catalytic site. Tight binding by the lesion-recognition pocket in addition to Mg2+ and hydrogen-bonding interactions to the DNA ends stabilize the product complex, suggesting an orderly recruitment of downstream proteins in this base-repair pathway.

The structure of the 1:1 complex of deoxycholate (3α,12α-dihydroxy-5β-cholan-24-oate, C 24 H 39 O 4 - , DCA - ) and tris(hydroxymethyl)methylammonium [(CH 2 OH) 3 CNH + 3 or C 4 H 12 NO + 3 , TRIS + ] has been determined. The crystal structure is one of four known where DCA exists in the monoclinic space group P2 1 . The side-chain conformation of DCA is synclinal, which is coupled with a half-chair conformation of ring D. The asymmetric unit contains one DCA- anion, one TRIS + cation and three water molecules.

A general one-pot synthetic route for mixed methyl−aryl Pt(II) diimine complexes is described. Performing the alkylation in neat Me_2S instead of ether or THF greatly reduces the amount of comproportionation products otherwise formed, diminishes separation problems, and improves yields. Treatment of the intermediate methyl−aryl complexes (Me_2S)_2Pt(Me)(Ar) with diimines (N−N) furnishes the methyl−aryl Pt(II) diimine complexes (N−N)Pt(Me)(Ar) in 76−84% yields. The Pt methyl−phenyl complex [p-Tol-N ═ VC(Me)C(Me) ═ N-p-Tol]Pt(Me)(Ph) has been characterized by X-ray diffraction.

Many Gram-positive bacteria produce ribosomally synthesized antimicrobial peptides, often termed bacteriocins. Genes encoding pediocin-like bacteriocins are generally cotranscribed with or in close vicinity to a gene encoding a cognate immunity protein that protects the bacteriocin-producer from their own bacteriocin. We present the first crystal structure of a pediocin-like immunity protein, EntA-im, conferring immunity to the bacteriocin enterocin A. Determination of the structure of this 103-amino acid protein revealed that it folds into an antiparallel four-helix bundle with a flexible C-terminal part. The fact that the immunity protein conferring immunity to carnobacteriocin B2 also consists of a four-helix bundle (Sprules, T., Kawulka, K. E., and Vederas, J. C. (2004) Biochemistry 43, 11740-11749) strongly indicates that this is a conserved structural motif in all pediocin-like immunity proteins. The C-terminal half of the immunity protein contains a region that recognizes the C-terminal half of the cognate bacteriocin, and the flexibility in the C-terminal end of the immunity protein might thus be an important characteristic that enables the immunity protein to interact with its cognate bacteriocin. By homology modeling of three other pediocin-like immunity proteins and calculation of the surface charge distribution for EntA-im and the three structure models, different charge distributions were observed. The differences in the latter part of helix 3, the beginning of helix 4, and the loop connecting these helices might also be of importance in determining the specificity.

This redetermination of l-isoleucine, C6H13NO2, forms part II of the series the crystal structures of hydrophobic amino acids. Standard deviations for bond lengths between heavy atoms are down to 0.002 A. Detailed parameters for the hydrogen-bonding pattern are given.

A series of novel half-sandwich M(I) and M(III) complexes (M = Co, Rh) bearing the N-heterocyclic carbene ligand 1,3-dimesitylimidazol-2-ylidene (IMes) have been prepared and characterized. Thus, (eta5-C(5)R(5))M(IMes)(C(2)H(4))(M = Co, Rh; R = H, Me) were obtained from the corresponding bis(ethene) complexes (eta5-C(5)R(5))M(C(2)H(4))(2), except for CpRh(IMes)(C(2)H(4)) which was prepared via the novel 16-electron Rh(I) compound Rh(IMes)(C(2)H(4))(2)Cl. The carbonyl compounds (eta5-C(5)R(5))Co(IMes)(CO)(R = H, Me) were synthesized by thermal CO substitution of (eta5-C(5)R(5))Co(CO)(2). A diamagnetic, apparently 16-electron Co(III) compound [CpCo(IMes)I](+)[I(3)(-)] was obtained from CpCo(IMes)(CO) and I(2). Finally, Co(III) and Rh(III) complexes CpCo(IMes)Me(2) and Cp*Rh(IMes)Me(2) were prepared by methylation of [CpCo(IMes)I](+)[I(3)(-)], and ligand exchange at Cp*Rh(Me(2)SO)Me(2), respectively. The molecular structures of CpCo(IMes)(CO), CpRh(IMes)(C(2)H(4)), Cp*Rh(IMes)(C(2)H(4)), and Cp*Rh(IMes)Me(2) were determined by single crystal X-ray diffraction. Steric and electronic factors imposed by the strongly donating and sterically demanding IMes ligand are discussed on the basis of X-ray crystallographic, NMR, and IR spectroscopic analyses. Very poor correlations are found between values for (1)J(Rh-C(carbene)) and dRh-C(carbene) data for Rh(i) N,N-heterocyclic carbene complexes including literature data and this work.

The peptide bond in the crystal structure of the title compound, C8H16N2O4, deviates substantially from planarity in the same manner as in other l-Ser-l-Xaa dipeptides, where Xaa is a hydro­phobic residue.

Crystals of the bacterial enterocin A immunity protein have been prepared by the hanging-drop vapour-diffusion technique at 293 K. The crystals diffract to better than 1.7 A resolution and X-ray diffraction data to 1.65 A have been collected at 110 K using synchrotron radiation. The enterocin A immunity protein crystals belong to the monoclinic crystal system, with unit-cell parameters a = 116.32, b = 42.35, c = 66.17 A, beta = 111.3 degrees. The symmetry and systematic absences in the diffraction pattern are consistent with space group C2. The presence of two molecules in the asymmetric unit with a molecular weight of approximately 12.2 kDa gives a crystal volume per protein mass (V(M)) of approximately 3.1 A(3) Da(-1) and a solvent content of approximately 60% by volume.

The three-dimensional structure of four malate dehydrogenases (MDH) from thermophilic and mesophilic phototropic bacteria have been determined by X-ray crystallography and the corresponding structures compared. In contrast to the dimeric quaternary structure of most MDHs, these MDHs are tetramers and are structurally related to tetrameric malate dehydrogenases from Archaea and to lactate dehydrogenases. The tetramers are dimers of dimers, where the structures of each subunit and the dimers are similar to the dimeric malate dehydrogenases. The difference in optimal growth temperature of the corresponding organisms is relatively small, ranging from 32 to 55 degrees C. Nevertheless, on the basis of the four crystal structures, a number of factors that are likely to contribute to the relative thermostability in the present series have been identified. It appears from the results obtained, that the difference in thermostability between MDH from the mesophilic Chlorobium vibrioforme on one hand and from the moderate thermophile Chlorobium tepidum on the other hand is mainly due to the presence of polar residues that form additional hydrogen bonds within each subunit. Furthermore, for the even more thermostable Chloroflexus aurantiacus MDH, the use of charged residues to form additional ionic interactions across the dimer-dimer interface is favored. This enzyme has a favorable intercalation of His-Trp as well as additional aromatic contacts at the monomer-monomer interface in each dimer. A structural alignment of tetrameric and dimeric prokaryotic MDHs reveal that structural elements that differ among dimeric and tetrameric MDHs are located in a few loop regions.

The biological conversions of O(2) and peroxides to water as well as certain incorporations of oxygen atoms into small organic molecules can be catalyzed by metal ions in different clusters or cofactors. The catalytic cycle of these reactions passes through similar metal-based complexes in which one oxygen- or peroxide-derived oxygen atom is coordinated to an oxidized form of the catalytic metal center. In haem-based peroxidases or oxygenases the ferryl (Fe(IV)O) form is important in compound I and compound II, which are two and one oxidation equivalents higher than the ferric (Fe(III)) form, respectively. In this study we report the 1.35 A structure of a compound II model protein, obtained by reacting hydrogen peroxide with ferric myoglobin at pH 5.2. The molecular geometry is virtually unchanged compared to the ferric form, indicating that these reactive intermediates do not undergo large structural changes. It is further suggested that at low pH the dominating compound II resonance form is a hydroxyl radical ferric iron rather than an oxo-ferryl form, based on the short hydrogen bonding to the distal histidine (2.70 A) and the Fe...O distance. The 1.92 A Fe...O distance is in agreement with an EXAFS study of compound II in horseradish peroxidase.

The C α -C'-N-C α (ω) torsion angle of the peptide bond in the crystal structure of the title compound, C 5 H 16 N 2 O 4 , is 157.37(15)°. This is the second-largest deviation from planarity observed for a small linear peptide.

Ab initio prediction of the crystal packing in complexes between two flexible molecules is a particularly challenging computational chemistry problem. In this work we present results of single crystal structure determinations as well as theoretical predictions for three 1 ratio 1 complexes between hydrophobic l- and d-amino acids (pseudoracemates), known from previous crystallographic work to form structures with one of two alternative hydrogen bonding arrangements. These are accurately reproduced in the theoretical predictions together with a series of patterns that have never been observed experimentally. In this bewildering forest of potential polymorphs, hydrogen bonding arrangements and molecular conformations, the theoretical predictions succeeded, for all three complexes, in finding the correct hydrogen bonding pattern. For two of the complexes, the calculations also reproduce the exact space group and side chain orientations in the best ranked predicted structure. This includes one complex for which the observed crystal packing clearly contradicted previous experience based on experimental data for a substantial number of related amino acid complexes. The results highlight the significant recent advances that have been made in computational methods for crystal structure prediction.