Effects of different black soldier fly larvae products on slow-growing broiler performance and carcass characteristics

Black soldier fly (BSF) larvae have gained significant attention as ingredients for poultry feed to improve value chain circularity and sustainability. Black soldier fly larvae contain bioactive compounds which can potentially improve broiler health and thereby performance. However, the functionality of bioactive compounds likely depends on how larvae are processed prior to feeding and to which extent larvae products are included in the diet. This may explain the variable results reported in literature on broiler performance and carcass characteristics when feeding them different types of BSF larvae products at different inclusion levels. Therefore, the present research aimed to investigate the effects of different BSF larvae products and inclusion levels in diets on performance and carcass characteristics of slow-growing broilers. The experiment started with 1,728 one-day-old slow-growing male broilers (Hubbard JA757). Nine dietary treatments were used, each replicated eight times. One group of broilers was given a control diet. The following BSF larvae products were investigated: live larvae, a combination of BSF larvae meal and oil mimicking the nutritional composition of the live larvae, and BSF larvae meal and oil separately. All insect products were tested at two inclusion levels. All diet programs were nutritionally comparable (isoenergetic and based on balanced levels of digestible essential amino acids). During the 7-wk trial, several performance parameters and carcass characteristics were measured. The results show that comparable or better broiler performance was achieved with the inclusion of BSF larvae products in the diets compared to the control. Based on the feed conversion ratio (FCR), the unprocessed larvae product and the highest inclusion level led to the most favorable results. Carcass characteristics remained unchanged when BSF larvae products were used in the diets compared to the control group, indicating favorable production output. The BSF larvae products investigated seem suitable feed ingredients for broilers at the current levels tested, generating performance benefits.

Conformations of the sugar-phosphate backbone in helical DNA crystal structures

The DNA backbone geometry was analyzed for 96 crystal structures of oligodeoxynucleotides. The ranges and mean values of the torsion angles for the observed subclasses of the A-, B-, and Z-DNA conformational types were determined by analyzing distributions of the torsion angles and scattergrams relating pairs of angles.

New parameters for the refinement of nucleic acid-containing structures

Structures at atomic resolution (up to 1.0 A) which contain bases, sugars or the phosphodiester linkage, were selected from the Nucleic Acid Database or the Cambridge Structural Database to build a nucleic acid dictionary from X-ray refined structures. The dictionary consists of the average values for bond distances, bond angles and dihedral angles. The variance of the sample is used to provide information about the expected r.m.s. deviations of the refined parameters. A dictionary was constructed for refinement trials in X-PLOR. The dictionary includes RNA and DNA in C2'-endo and C3'-endo sugar pucker conformations, as well as values for the backbone dihedrals. Tests were performed on the dictionary using three structures: a B-DNA, a Z-DNA and a protein-DNA complex. During the course of refinement, all three structures showed significant improvements as measured by r.m.s. deviations and R factors when compared to the previous DNA dictionary.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: DNA binding specificity based on energetics of DNA kinking

The catabolite activator protein (CAP) makes no direct contact with the consensus base-pair T:A at position 6 of the DNA half-site 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' but, nevertheless, exhibits strong specificity for T:A at position 6. Binding of CAP results in formation of a sharp DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site. The consensus base-pair T:A at position 6 and the consensus base-pair G:C at position 7 form a T:A/G:C step, which is known to be associated with DNA flexibility. It has been proposed that specificity for T:A at position 6 is a consequence of formation of the DNA kink between positions 6 and 7, and of effects of the T:A(6)/G:C(7) step on the geometry of DNA kinking, or the energetics of DNA kinking. In this work, we determine crystallographic structures of CAP-DNA complexes having the consensus base-pair T:A at position 6 or the non-consensus base-pair C:G at position 6. We show that complexes containing T:A or C:G at position 6 exhibit similar overall DNA bend angles and local geometries of DNA kinking. We infer that indirect readout in this system does not involve differences in the geometry of DNA kinking but, rather, solely differences in the energetics of DNA kinking. We further infer that the main determinant of DNA conformation in this system is protein-DNA interaction, and not DNA sequence.

Indirect readout of DNA sequence at the primary-kink site in the CAP-DNA complex: alteration of DNA binding specificity through alteration of DNA kinking

The catabolite activator protein (CAP) sharply bends DNA in the CAP-DNA complex, introducing a DNA kink, with a roll angle of approximately 40 degrees and a twist angle of approximately 20 degrees, between positions 6 and 7 of the DNA half-site, 5'-A(1)A(2)A(3)T(4)G(5)T(6)G(7)A(8)T(9)C(10)T(11)-3' ("primary kink"). CAP recognizes the base-pair immediately 5' to the primary-kink site, T:A(6), through an "indirect-readout" mechanism involving sequence effects on the energetics of primary-kink formation. CAP recognizes the base-pair immediately 3' to the primary-kink site, G:C(7), through a "direct-readout" mechanism involving formation of a hydrogen bond between Glu181 of CAP and G:C(7). Here, we report that substitution of the carboxylate side-chain of Glu181 of CAP by the one-methylene-group-shorter carboxylate side-chain of Asp changes DNA binding specificity at position 6 of the DNA half site, changing specificity for T:A(6) to specificity for C:G(6), and we report a crystallographic analysis defining the structural basis of the change in specificity. The Glu181-->Asp substitution eliminates the primary kink and thus eliminates indirect-readout-based specificity for T:A(6). The Glu181-->Asp substitution does not eliminate hydrogen-bond formation with G:C(7), and thus does not eliminate direct-readout-based specificity for G:C(7).

The crystal and molecular structure of a collagen-like peptide with a biologically relevant sequence

A detailed description of the 2.0 A structure of the triple-helical peptide, (Pro-Hyp-Gly)(3)-Ile-Thr-Gly-Ala-Arg-Gly-Leu-Ala-Gly-Pro-Hyp-Gly-(Pro-Hyp-Gly)(3), denoted as T3-785, is presented. This peptide contains a biologically relevant sequence and was designed to model the imino acid-poor 785-796 region of human type III collagen just C-terminal to the matrix metalloproteinase cleavage site. The crystal structure of the T3-785 peptide demonstrates that sequence can influence local conformational changes in triple-helical structure, in terms of superhelical pitch, hydrogen bonding pattern, and hydration patterns. The novel packing arrangement displayed by the T3-785 structure, compared with those of collagen-like peptides with more imino acid-rich sequences indicates the sequence dependence of intermolecular assemblies in collagen as well. The observed synergy between the packing arrangements and the extended hydration network indicates that hydration of the triple helix is directly related to its association with other molecules.

Checking nucleic acid crystal structures

The program SFCHECK [Vaguine et al. (1999), Acta Cryst. D55, 191-205] is used to survey the quality of the structure-factor data and the agreement of those data with the atomic coordinates in 105 nucleic acid crystal structures for which structure-factor amplitudes have been deposited in the Nucleic Acid Database [NDB; Berman et al. (1992), Biophys. J. 63, 751-759]. Nucleic acid structures present a particular challenge for structure-quality evaluations. The majority of these structures, and DNA molecules in particular, have been solved by molecular replacement of the double-helical motif, whose high degree of symmetry can lead to problems in positioning the molecule in the unit cell. In this paper, the overall quality of each structure was evaluated using parameters such as the R factor, the correlation coefficient and various atomic error estimates. In addition, each structure is characterized by the average values of several local quality indicators, which include the atomic displacement, the density correlation, the B factor and the density index. The latter parameter measures the relative electron-density level at the atomic position. In order to assess the quality of the model in specific regions, the same local quality indicators are also surveyed for individual groups of atoms in each structure. Several of the global quality indicators are found to vary linearly with resolution and less than a dozen structures are found to exhibit values significantly different from the mean for these indicators, showing that the quality of the nucleic acid structures tends to be rather uniform. Analysis of the mutual dependence of the values of different local quality indicators, computed for individual residues and atom groups, reveals that these indicators essentially complement each other and are not redundant with the B factor. Using several of these indicators, it was found that the atomic coordinates of the nucleic acid bases tend to be better defined than those of the backbone. One of the local indicators, the density index, is particularly useful in spotting regions of the model that fit poorly in the electron density. Using this parameter, the quality of crystallographic water positions in the analyzed structures was surveyed and it was found that a sizable fraction of these positions have poorly defined electron density and may therefore not be reliable. The possibility that cases of poorly positioned water molecules are symptomatic of more widespread problems with the structure as a whole is also raised.

Protein-RNA interactions: a structural analysis

A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level.

The PDB data uniformity project

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.

The Protein Data Bank and the challenge of structural genomics

The PDB has created systems for the processing, exchange, query, and distribution of data that will enable many aspects of high throughput structural genomics.

Staggered molecular packing in crystals of a collagen-like peptide with a single charged pair

The crystal structure of the triple-helical peptide, (Pro-Hyp-Gly)(4)-Glu-Lys-Gly-(Pro-Hyp-Gly)(5) has been determined to 1.75 A resolution. This peptide was designed to examine the effect of a pair of adjacent, oppositely charged residues on collagen triple-helical conformation and intermolecular interactions. The molecular conformation (a 7(5) triple helix) and hydrogen bonding schemes are similar to those previously reported for collagen triple helices and provides a second instance of water mediated N--H . . . O==C interchain hydrogen bonds for the amide group of the residue following Gly. Although stereochemically capable of forming intramolecular or intermolecular ion pairs, the lysine and glutamic acid side-chains instead display direct interactions with carbonyl groups and hydroxyproline hydroxyl groups or interactions mediated by water molecules. Solution studies on the EKG peptide indicate stabilization at neutral pH values, where both Glu and Lys are ionized, but suggest that this occurs because of the effects of ionization on the individual residues, rather than ion pair formation. The EKG structure suggests a molecular mechanism for such stabilization through indirect hydrogen bonding. The molecular packing in the crystal includes an axial stagger between molecules, reminiscent of that observed in D-periodic collagen fibrils. The presence of a Glu-Lys-Gly triplet in the middle of the sequence appears to mediate this staggered molecular packing through its indirect water-mediated interactions with backbone C==O groups and side chains.

Crystal studies of B-DNA: the answers and the questions

The history of DNA crystallography is reviewed and is followed by discussion of the methods used for structure determination. The features of B-DNA molecular and crystal structures are described.

Integrin-collagen complex: a metal-glutamate handshake

The recently determined crystal structure of the complex between an integrin I domain and a synthetic collagen peptide shows a collagen triple-helix engaged in specific macromolecular recognition and binding. This structure confirms a previously proposed binding mechanism for integrin I domains and has important implications for integrin activation and signalling.

An overview of the structures of protein-DNA complexes

On the basis of a structural analysis of 240 protein-DNA complexes contained in the Protein Data Bank (PDB), we have classified the DNA-binding proteins involved into eight different structural/functional groups, which are further classified into 54 structural families. Here we present this classification and review the functions, structures and binding interactions of these protein-DNA complexes.

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

Sequence dependent conformational variations of collagen triple-helical structure

The 2 A crystal structure reported here of the collagen-like model peptide, T3-785, provides the first visualization of how the sequence of collagen defines distinctive local conformational variations in triple-helical structure.

Protein-DNA interactions: A structural analysis

A detailed analysis of the DNA-binding sites of 26 proteins is presented using data from the Nucleic Acid Database (NDB) and the Protein Data Bank (PDB). Chemical and physical properties of the protein-DNA interface, such as polarity, size, shape, and packing, were analysed. The DNA-binding sites shared common features, comprising many discontinuous sequence segments forming hydrophilic surfaces capable of direct and water-mediated hydrogen bonds. These interface sites were compared to those of protein-protein binding sites, revealing them to be more polar, with many more intermolecular hydrogen bonds and buried water molecules than the protein-protein interface sites. By looking at the number and positioning of protein residue-DNA base interactions in a series of interaction footprints, three modes of DNA binding were identified (single-headed, double-headed and enveloping). Six of the eight enzymes in the data set bound in the enveloping mode, with the protein presenting a large interface area effectively wrapped around the DNA.A comparison of structural parameters of the DNA revealed that some values for the bound DNA (including twist, slide and roll) were intermediate of those observed for the unbound B-DNA and A-DNA. The distortion of bound DNA was evaluated by calculating a root-mean-square deviation on fitting to a canonical B-DNA structure. Major distortions were commonly caused by specific kinks in the DNA sequence, some resulting in the overall bending of the helix. The helix bending affected the dimensions of the grooves in the DNA, allowing the binding of protein elements that would otherwise be unable to make contact. From this structural analysis a preliminary set of rules that govern the bending of the DNA in protein-DNA complexes, are proposed.

The past and future of structure databases

For many years the primary source of information about biological macromolecules was the Protein Data Bank, which is a repository of files containing coordinates of biological macromolecules. Now a variety of databases has been developed in which structures are organized in different ways. Currently available are databases that classify molecules according to their overall structural characteristics or particular features of structures, as well as databases that focus on particular protein families in depth.

The crystal structure of an autoprocessed Ser221Cys-subtilisin E-propeptide complex at 2.0 A resolution

We report here the crystallographic structure determination of an autoprocessed (Ser221Cys)-subtilisin E-propeptide complex at 2.0 A resolution. The subtilisin domain sequence has a single substitution (Ser221Cys) which has been shown to block the maturation process prior to degradation of the propeptide domain (77 residues) that acts as an intramolecular chaperon. This mutation, however, did not prevent the enzyme from cleaving its propeptide domain with a 60-80% efficiency. The current determination is the first example of a subtilisin E-propeptide complex which has been autoprocessed. A previous structure determination of a BPN'-prosegment complex has been reported in which the subtilisin domain was extensively mutated and a calcium binding loop was deleted. Further, in this earlier determination, the complex was formed by the addition of separately expressed propeptide domain. The structure determination reported here provides additional information about the nature of the interaction between the subtilisin and propeptide domains in this complex.

Hydration of the phosphate group in double-helical DNA

Water distributions around phosphate groups in 59 B-, A-, and Z-DNA crystal structures were analyzed. It is shown that the waters are concentrated in six hydration sites per phosphate and that the positions and occupancies of these sites are dependent on the conformation and type of nucleotide. The patterns of hydration that are characteristic of the backbone of the three DNA helical types can be attributed in part to the interactions of these hydration sites.

The Nucleic Acid Database: A resource for nucleic acid science

The Nucleic Acid Database (NDB) distributes information about nucleic acid-containing structures. Here the information content of the database as well as the query capabilities are described. A summary of how the technology developed by this project has been used to develop other macromolecular databases is given.

An analysis of the relationship between hydration and protein-DNA interactions

Eleven protein-DNA crystal structures were analyzed to test the hypothesis that hydration sites predicted in the first hydration shell of DNA mark the positions where protein residues hydrogen-bond to DNA. For nine of those structures, protein atoms, which form hydrogen bonds to DNA bases, were found within 1.5 A of the predicted hydration positions in 86% of the interactions. The correspondence of the predicted hydration sites with the hydrogen-bonded protein side chains was significantly higher for bases inside the conserved DNA recognition sequences than outside those regions. In two CAP-DNA complexes, predicted base hydration sites correctly marked 71% (within 1.5 A) of protein atoms, which form hydrogen bonds to DNA bases. Phosphate hydration was compared to actual protein binding sites in one CAP-DNA complex with 78% marked contacts within 2.0 A. These data suggest that hydration sites mark the binding sites at protein-DNA interfaces.

Maximum A posteriori classification of DNA structure from sequence information

We introduce an algorithm, LLLAMA, which combines simple pattern recognizers into a general method for estimating the entropy of a sequence. Each pattern recognizer exploits a partial match between subsequences to build a model of the sequence. Since the primary features of interest in biological sequence domains are subsequences with small variations in exact composition, LLLAMA is particularly suited to such domains. We describe two methods, LLLAMA-length and LLLAMA-alone, which use this entropy estimate to perform maximum a posteriori classification. We apply these methods to several problems in three-dimensional structure classification of short DNA sequences. The results include a surprisingly low 3.6% error rate in predicting helical conformation of oligonucleotides. We compare our results to those obtained using more traditional methods for automated generation of classifiers.

X-ray crystallographic determination of a collagen-like peptide with the repeating sequence (Pro-Pro-Gly)

The crystal structure of the triple-helical peptide (Pro-Pro-Gly)10 has been re-determined to obtain a more accurate description for this widely studied collagen model and to provide a comparison with the recent high-resolution crystal structure of a collagen-like peptide containing Pro-Hyp-Gly regions. This structure demonstrated that hydroxyproline participates extensively in a repetitive hydrogen-bonded assembly between the peptide and the solvent molecules. Two separate structural studies of the peptide (Pro-Pro-Gly)10 were performed with different crystallization conditions, data collection temperatures, and X-ray sources. The polymer-like structure of one triple-helical repeat of Pro-Pro-Gly has been determined to 2.0 A resolution in one case and 1.7 A resolution in the other. The solvent structures of the two peptides were independently determined specifically for validation purposes. The two structures display a reverse chain trace compared with the original structure determination. In comparison with the Hyp-containing peptide, the two Pro-Pro-Gly structures demonstrate very similar molecular conformation and analogous hydration patterns involving carbonyl groups, but have different crystal packing. This difference in crystal packing indicates that the involvement of hydroxyproline in an extended hydration network is critical for the lateral assembly and supermolecular structure of collagen.

Crystal structure of the unique RNA-binding domain of the influenza virus NS1 protein

The nonstructural protein (NS1 protein) of the influenza A virus binds to several types of RNAs. X-ray crystallographic analysis of the RNA-binding domain reveals a unique topology for the monomer as well as a novel six-helix structure for the dimer.

Crystallographic evidence for C alpha-H...O=C hydrogen bonds in a collagen triple helix

The crystal structure of the collagen triple-helical peptide (Pro-Hyp-Gly)4-Pro-Hyp-Ala-(Pro-Hyp-Gly)5 shows evidence for the existence of interchain contacts between alpha-carbon hydrogens from Gly and Hyp residues, and carbonyl groups from Gly and Pro residues on neighboring chains. The geometrical disposition of these contacts makes it reasonable to describe them as C alpha-H...O=C hydrogen bonds. Two repetitive patterns can be identified, and one of them is identical to a similar type of interaction reported recently for beta-sheets in globular proteins, which suggests a more universal character for C-H...O hydrogen bonds in building protein secondary structure elements. They are presumably much weaker in energy than the interchain N-H...O=C hydrogen bonds responsible for the alignment of the three chains in the collagen triple helix, and therefore their contribution will be a small but cooperative decrease on the total interchain hydrogen bonding energy.

Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface

The crystallographic structure of the CAP-DNA complex at 3.0 A resolution has been reported previously. For technical reasons, the reported structure had been determined using a gapped DNA molecule lacking two phosphates important for CAP-DNA interaction. In this work, we report the crystallographic structure of the CAP-DNA complex at 2.5 A resolution using a DNA molecule having all phosphates important for CAP-DNA interaction. The present resolution permits unambiguous identification of amino acid-base and amino acid-phosphate hydrogen bonded contacts in the CAP-DNA complex. In addition, the present resolution permits accurate definition of the kinked DNA conformation in the CAP-DNA complex.

Crystallization, X-ray studies, and site-directed cysteine mutagenesis of the DNA-binding domain of OmpR

A C-terminal fragment of the transcription factor OmpR has been crystallized using the sitting drop vapor-diffusion method. Crystals belong to the trigonal space-group P3n12 with cell dimensions a = b = 54.4 A, c = 135.5 A, and gamma = 120.00 degrees. A second crystal form has been obtained by soaking this crystal form in a cryo-buffer and flash-cooling to 108 K in a cold nitrogen stream. Crystals belong to the trigonal space-group P3n12 with cell dimensions a = b = 108.07 A, c = 131.81 A, and gamma = 120.00 degrees. Both crystal forms diffract to at least 2.3 A at a synchrotron light source. Single-site cysteine mutations have been introduced to provide mercury-binding sites for multiple isomorphous replacement.

Nucleic acid crystallography: a view from the nucleic acid database

What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB.

Disrupted collagen architecture in the crystal structure of a triple-helical peptide with a Gly-->Ala substitution

The crystal structure of the collagen-based peptide (Pro-Hyp-Gly)4-Pro-Hyp-Ala-(Pro-Hyp-Gly)5 has provided for the first time a highly detailed picture of the architectural elements that come into play in the collagen triple helix. The center of the molecule, which harbors a Gly-->Ala substitution, shows subtle conformational changes that result in a local untwisting of the triple helix. The characteristic hydrogen bonding pattern of collagen triple helices is replaced by interstitial water bridges. These effects may be relevant to the diseased states derived from Gly-->X mutations in collagens. The possible implications of this disrupted architecture for collagen assemblies are discussed.

Structure of a new crystal form of a DNA dodecamer containing T.(O6Me)G base pairs

The structure of the synthetic dodecamer (d[CGTGAATTC(O6Me)GCG])2 has been determined to a resolution of 2.25 A and refined to a final R factor of 16.7%. The volume of the unit cell is significantly smaller by 16% than the original Drew and Dickerson parent dodecamer [Drew, H. R., Wing, R. M., Takano, T., Broka, C., Tanaka, S., Itakura, K., & Dickerson, R. E. (1981) Proc. Natl. Acad. Sci. U.S.A. 78, 7318-7322]. The double helix is in a different position in the unit cell, rotated by -85.9 degrees, and translated by 9.9 A around the helical axis with respect to the parent structure. The intermolecular arrangement of helices, characterized by double hydrogen bonded guanine-guanine minor groove interactions, remains conserved. The molecular geometry exhibits several significant changes that are related to the changed position of the helix and the presence of two mismatched base pairs with O6-methylguanine. Both mispairs are found in a symmetrical T(anti).(O6Me)G(anti) conformation, and the methyl groups are in proximal orientation. The hydration pattern of the structure is different and can be related to changes in the minor groove geometry. An incorrect model that was isomorphous to the parent dodecamer could be refined to a low R factor. Characteristics of the refinement and of the geometry that are indicative of incorrect structures have been analyzed.

Hydration of the DNA bases is local

Ordered hydration sites were determined for the nucleotide bases in B-type conformations using the crystal structure data on 14 B-DNA decamer structures. A method of density representation was extended so that positions, occupancies, and distributions of the hydration sites were predicted around a B-DNA double helix by a method analogous to crystallographic refinement. The predicted hydration sites correctly reproduce the main features of hydration around the B-DNA dodecamer. In contrast to the previous observations, the newly available crystal data show the same extent of hydration of guanine and adenine, and of cytosine and thymine.

Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative

The three-dimensional structure of d[CGTA'CG], where A' = [2-NH2-A], was determined to atomic (1.35 A) resolution by single isomorphous replacement. The d[CGTA'CG] hexamer crystallizes in space group P3221, and is not isomorphous with other DNA hexanucleotides. Despite completely different crystal packing, the essential characteristics of the Z-DNA conformation are maintained. The structure was determined by single isomorphous replacement using a triammine platinum fragment. Thus, this study also demonstrates, for the first time, the feasibility of the use of this reagent for the direct phasing of DNA crystal structures.

Crystal structure of a DNA decamer showing a novel pseudo four-way helix-helix junction

The crystal structure of the decanucleotide d(CGCAATTGCG)2 has been solved by a combination of molecular replacement and heavy-atom procedures and has been refined to an R factor of 20.2% at 2.7 A. It is not a fully base-paired duplex but has a central core of eight Watson-Crick base pairs flanked by unpaired terminal guanosines and cytosines. These participate in hydrogen-bonding arrangements with adjacent decamer duplexes in the crystal lattice. The unpaired guanosines are bound in the G+C regions of duplex minor grooves. The cytosines have relatively high mobility, even though they are constrained to be in one region where they are involved in base-paired triplets with G.C base pairs. The 5'-AATT sequence in the duplex region has a narrow minor groove, providing further confirmation of the sequence-dependent nature of groove width.

Hydration structure of a collagen peptide

BACKGROUND

The collagen triple helix is a unique protein motif defined by the supercoiling of three polypeptide chains in a polyproline II conformation. It is a major domain of all collagen proteins and is also reported to exist in proteins with host defense function and in several membrane proteins. The triple-helical domain has distinctive properties. Collagen requires a high proportion of the post-translationally modified imino acid 4-hydroxyproline and water to stabilize its conformation and assembly. The crystal structure of a collagen-like peptide determined to 1.85 Angstrum showed that these two features may be related.

RESULTS

A detailed analysis of the hydration structure of the collagen-like peptide is presented. The water molecules around the carbonyl and hydroxyprolyl groups show distinctive geometries. There are repetitive patterns of water bridges that link oxygen atoms within a single peptide chain, between different chains and between different triple helices. Overall, the water molecules are organized in a semi-clathrate-like structure that surrounds and interconnects triple helices in the crystal lattice. Hydroxyprolyl groups play a crucial role in the assembly.

CONCLUSIONS

The roles of hydroxyproline and hydration are strongly interrelated in the structure of the collagen triple helix. The specific, repetitive water bridges observed in this structure buttress the triple-helical conformation. The extensively ordered hydration structure offers a good model for the interpretation of the experimental results on collagen stability and assembly.

Analysis of local helix bending in crystal structures of DNA oligonucleotides and DNA-protein complexes

Sequence-dependent bending of the helical axes in 112 oligonucleotide duplex crystal structures resident in the Nucleic Acid Database have been analyzed and compared with the use of bending dials, a computer graphics tool. Our analysis includes structures of both A and B forms of DNA and considers both uncomplexed forms of the double helix as well as those bound to drugs and proteins. The patterns in bending preferences in the crystal structures are analyzed by base pair steps, and emerging trends are noted. Analysis of the 66 B-form structures in the Nucleic Acid Database indicates that uniform trends within all pyrimidine-purine and purine-pyrimidine steps are not necessarily observed but are found particularly at CG and GC steps of dodecamers. The results support the idea that AA steps are relatively straight and that larger roll bends occur at or near the junctions of these A-tracts with their flanking sequences. The data on 16 available crystal structures of protein-DNA complexes indicate that the majority of the DNA bends induced via protein binding are sharp localized kinks. The analysis of the 30 available A-form DNA structures indicates that these structures are also bent and show a definitive preference for bending into the deep major groove over the shallow minor groove.

Crystal and molecular structure of a collagen-like peptide at 1.9 A resolution

The structure of a protein triple helix has been determined at 1.9 angstrom resolution by x-ray crystallographic studies of a collagen-like peptide containing a single substitution of the consensus sequence. This peptide adopts a triple-helical structure that confirms the basic features determined from fiber diffraction studies on collagen: supercoiling of polyproline II helices and interchain hydrogen bonding that follows the model II of Rich and Crick. In addition, the structure provides new information concerning the nature of this protein fold. Each triple helix is surrounded by a cylinder of hydration, with an extensive hydrogen bonding network between water molecules and peptide acceptor groups. Hydroxyproline residues have a critical role in this water network. The interaxial spacing of triple helices in the crystal is similar to that in collagen fibrils, and the water networks linking adjacent triple helices in the crystal structure are likely to be present in connective tissues. The breaking of the repeating (X-Y-Gly)n pattern by a Gly-->Ala substitution results in a subtle alteration of the conformation, with a local untwisting of the triple helix. At the substitution site, direct interchain hydrogen bonds are replaced with interstitial water bridges between the peptide groups. Similar conformational changes may occur in Gly-->X mutated collagens responsible for the diseases osteogenesis imperfecta, chondrodysplasias, and Ehlers-Danlos syndrome IV.

Platinum(II) triamine complexes: cis-[PtCl(NH3)2(C10H13N5O5)]NO3.2H2O and [PtCl(C2H8N2)(C4H6N2)]NO3

The structures of cis-diamminechloro(guanosine-N7)-platinum(II) nitrate dihydrate, cis-[PtCl(NH3)2-(C10H13N5O5)]NO3.2H2O, (I), and chloro(ethylenediamine)(1-methylimidazole-N3)platinum(II) nitrate, [PT-(C2H8N2)(C4H6N2)Cl]NO3, [PtCl(en)(1-MeIm)]NO3, (II), were determined by single-crystal X-ray diffraction. The former complex crystallized in the orthorhombic system and the latter in the monoclinic system. In compound (I), water molecules were found to connect the metal complex with the nitrate counter ions via hydrogen bonding.

Crystal structure of a mispaired dodecamer, d(CGAGAATTC(O6Me)GCG)2, containing a carcinogenic O6-methylguanine

The crystal structure of the synthetic deoxydodecamer d(CGAGAATTC(O6Me)GCG)2 has been determined and refined to an R-factor of 16.9% with data up to 2.9-A resolution. This sequence contains two mismatched base pairs between O6-methylguanine and adenine with the arrangement A(syn).(O6-Me)G(anti) which differs from the geometry observed in solution by NMR. The intermolecular arrangement is equivalent to the other isomorphous deoxydodecamers. However, the weakening of some significant crystal packing contacts was observed and related to the effect of stacking between the mispaired adenine and the adjacent guanine in the sequence. The structure is highly hydrated, with a total of 49 solvent molecules located. The methyl group and the mismatched base-pair geometry locally disrupt the B-DNA-type solvent network with two solvent molecules found close to the N1 and N6 of the mispaired adenine.

Crystal structure and NMR conformation of a cyclic pseudotetrapeptide containing urethane backbone linkages

Urethane bonds, derived from the hydroxyl group of the tyrosine side chain, have been investigated as a new type of amide bond mimetic in the design of pseudopeptides. The structure of a representative cyclic pseudotetrapeptide that consists of an -Ala-Tyr(urethane)Ala-Tyr(urethane) sequence fused into a rigid ring has been studied in the solid state by x-ray crystallography and in solution by two-dimensional nmr techniques. The cyclic pseudotetrapeptide has an oblong shape. The backbone urethane bonds assume a trans-trans conformation. The carbonyl groups in the ring have an alternating pattern of down, up, down, up with respect to the average ring plane. Solution nmr studies give observed nuclear Overhauser effects and coupling constants largely in agreement with the crystal structure. However, in solution the observed structure is likely to be conformationally averaged, and in the averaged structure, the urethane bond is perpendicular to the plane of the aromatic ring of the tyrosine, while in the crystal it is close to this plane. These differences may be explained by intermolecular hydrogen-bonding interactions. Four aspects of the conformation of the cyclic pseudotetrapeptide were investigated in detail: the tyrosine residue with the attached side-chain urethane bond (the tyrosine-urethane unit), the conformation of the two urethane backbone linkages, the conformation of the two conventional peptide bonds within this unusual ring structure, and the tight turns within the cyclic pseudotetrapeptide. The conformation of the tight turns present in the cyclic pseudotetrapeptide is very similar to that of a beta-bend of type II. Intermolecular hydrogen bonding, joining adjacent layers of the cyclic pseudotetrapeptide in the solid state, resemble a parallel beta-pleated sheet. The presence of these structural motifs in the cyclic pseudotetrapeptide indicates that the tyrosine urethane unit may find applications in peptide and protein engineering.

A systematic method for studying the spatial distribution of water molecules around nucleic acid bases

A new method to analyze the distribution of water molecules around the bases in DNA is presented. This method relies on the notion of a "hydrated building block," which represents the joint observed hydration around all bases of a particular type, in structures of a particular conformation type. The hydrated building blocks were constructed using atomic coordinates from 40 structures contained in the Nucleic Acid Database. Pseudoelectron densities were calculated for water molecules in each hydrated building block using standard crystallographic procedures. The electron densities were fitted to obtain "average building blocks," which represent bases with waters only at average or probable positions. Both types of building blocks were used to construct models of hydrated DNA oligomers. The essential features of the solvent structure around d(CGCGAATTCGCG)2 in the B form and d(CGCGCG)2 in the Z form were reproduced.

Structure of an interleukin-1 beta mutant with reduced bioactivity shows multiple subtle changes in conformation that affect protein-protein recognition

Site-specific mutagenesis was used to obtain the human interleukin-1 beta mutant protein with glycine substituted for threonine at position 9 (IL-1 beta Thr9Gly). The mutant maintains receptor binding but exhibits significantly reduced biological activity. The crystal structure of IL-1 beta Thr9Gly has been determined at 2.4-A resolution by molecular replacement techniques and refined to a crystallographic R-factor of 19.0%. IL-1 beta Thr9Gly crystallizes in a different space group (P6(5)22) than does native IL-1 beta (P4(3)); thus the molecules pack differently. Their overall structure is similar, nevertheless, with both composed of 153 amino acids which form 12 antiparallel beta-strands. However, significant conformational differences both close to and far from the site of the mutation may explain the mutant's altered properties.

Low temperature structures of dCpG-proflavine. Conformational and hydration effects

The structure of the complex of dCpG with proflavine was determined using x-ray data taken at -130 degrees C (low temperature) and at -2 degrees C (cold temperature) and compared with the structure of the complex determined previously at room temperature (Shieh, H. S., H. M. Berman, M. Dabrow, and S. Neidle. 1980. Nucleic Acids Res. 8:85-97). Low temperature was refined with 5,125 reflections between 8.0 and 0.93 A, Anisotropically modeled temperature factors were used for DNA/drug atoms and isotropic ones for water oxygens to R factor of 12.2% in P2(1)2(1)2; a = 32.853, b = 21.760, c = 13.296 A. Cold temperature was refined isotropically with 2,846 reflections 8.0-0.89 A to R = 15.1% in P2(1)2(1)2; a = 32.867, b = 22.356, c = 13.461 A. Both structures are very similar to the room temperature one, though some important differences were observed: one guanine sugar moiety is disordered and additional water molecules have been located that give rise to infinite polyhedral hydration networks.

Crystal and molecular structure of a DNA fragment containing a 2-aminoadenine modification: the relationship between conformation, packing, and hydration in Z-DNA hexamers

The crystal and molecular structure of d(CGUA'CG)2 (where A' is 2-aminoadenine) has been determined and refined to an R factor of 13.8% for data 8.0-1.3 A. The structure is very similar to the original Z-DNA structures with the sequence d(CGCGCG)2 [Gessner, R. V., Frederick, C. A., Quigley, G. J., Rich, A., & Wang, A. H.-J. (1989) J. Biol. Chem. 264, 7921] and shows that the substitution of 2-aminoadenine-uracil base pairs in the two central steps is consistent with Z-DNA formation. In addition, we show how waters mediating intermolecular interactions may help to explain the ZI-ZII conformational pattern found in many Z-DNA structures.

A structural model for sequence-specific proflavin-DNA interactions during in vitro frameshift mutagenesis

Molecular models describing intermediates that may lead to proflavin-induced 1 bp deletions during in vitro polymerization by E. coli DNA polymerase I Klenow fragment are proposed. The models provide structural explanations for the fact that the induced frameshifts always occur opposite template bases that are adjacent to 5' pyrimidines and are based on the underlying hypothesis that the deletions arise because the polymerase passes by a template base without copying it. Because the most frequent mutations are opposite Pu in the template sequence 5' Py Pu 3', a single-strand loop-out model was constructed for this sequence and proflavin was added, using structures found in crystalline oligonucleotides and their complexes with proflavin. The model seeks to rationalize the roles of the 5' pyrimidine and proflavin in facilitating the bypass. Four potential roles for proflavin in mutagenesis are described: 1) stacking on the looped-out base; 2) stacking on the base pair immediately preceding the site of mutation; 3) hydrogen bonding with the 5' pyrimidine; 4) hydrogen bonding with the phosphate backbone. These models point to the possibility that a number of proflavin-DNA interactions may be involved. In contrast, modeling does not suggest a role for classically intercalated proflavin in frameshift mutagenesis arising during in vitro DNA polymerization.