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H M Berman

Publications and source records attributed to H M Berman.

At least 37 records · Page 2Linked to original sources
PubMed1998

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.

Binding Sites↗
PubMed1998

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.

Binding Sites↗
PubMed1998

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.

Algorithms↗
PubMed1996

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.

Collagen↗
PubMed1996

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.

Base Composition↗
PubMed1996

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.

Journal Article↗
PubMed1996

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.

Amino Acid Sequence↗
PubMed1996

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.

Base Sequence↗
PubMed1996

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.

Alanine↗
PubMed1995

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.

Base Composition↗
PubMed1995

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.

Base Sequence↗
PubMed1995

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.

Base Composition↗
PubMed1995

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.

Alanine↗
PubMed1995

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.

Adenine↗