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M M Teeter

Publications and source records attributed to M M Teeter.

At least 37 records · Page 2Linked to original sources
PubMed1993

Patterns for prediction of hydration around polar residues in proteins.

The atomic co-ordinates of seven very high resolution (< 1.4 A) proteins have been used to define a water-hydrogen bond template for five polar side-chains (arginine, aspartic acid, glutamic acid, asparagine and glutamine). The average water molecule positions determined were consistent with the hydrogen bonding stereochemistry expected for each side-chain. Hydrogen bonding geometry around nitrogen atoms was significantly better localized than around oxygen atoms, perhaps because of the proton on nitrogen. A prediction algorithm written to locate water molecule sites around these side-chains from the protein co-ordinates only was tested for crambin as well as for two high resolution protein structures not included in the hydrogen bond data base. The root-mean-square deviation of the predicted positions from the crystallographically determined ones for these structures was better than the resolution of these structures. The method also successfully predicted water positions for X-ray refinement of two proteins, indicating that predicted water molecules are within the radius of convergence of refinement. This method has utility for X-ray models as well as for analysis of enzyme hydration and function.

Algorithms↗
PubMed1993

Improvement of turn structure prediction by molecular dynamics: a case study of alpha 1-purothionin.

Because of the problems in predicting a correct conformation for loop regions in homology-based prediction, disagreements are often found between the predicted models and the refined X-ray structures of the same protein in loop regions. Such a situation has been encountered for alpha 1-purothionin (alpha 1-PT). Hence, attempts have been made to improve the predicted model of alpha 1-PT by limited molecular dynamics using both AMBER and XPLOR. With molecular dynamics, the previously predicted incorrect turn region reverts to the correct conformation as seen in the X-ray refined structure. In contrast to the model which is not subjected to molecular dynamics, the improved model refines with the X-ray data of alpha 1-PT in fewer cycles, without any manual rebuilding and with comparable or better refinement statistics. Also, the improved model serves as a better starting model in the determination of the structure with the molecular replacement methods.

Antimicrobial Cationic Peptides↗
PubMed1992

Calmodulin binding to alpha 1-purothionin: solution binding and modeling of the complex.

CD and fluorescence spectroscopic measurements show that calmodulin (CaM) binds to purothionins (alpha 1-purothionin: alpha 1-PT; beta-purothionin: beta-PT) in 1:1 stoichiometry with an affinity similar to that exhibited with the tightest binding CaM-binding peptides. Using the available crystal structures of CaM and alpha 1-PT, a model has been built for the interaction of CaM and alpha 1-PT and subjected to potential energy minimization. In the model, there is a bend in the central helix of CaM similar to that suggested by Persechini and Kretsinger (J. Card. Pharm. 12:501-512, 1988). alpha 1-PT fits snugly into the cavity formed by the bent CaM molecule with each of its two helices making apolar interactions with each of the two hydrophobic clefts situated at the terminal domains of CaM. The complex is further stabilized by numerous polar and electrostatic interactions on the rims of the clefts. Our model is compared with two other similar models previously reported for the CaM complexes with other helical peptides and generalizations about the mode of CaM binding to target proteins are made, which have wide relevance to the function of CaM. By analogy, a similar model is predicted for a CaM-beta-PT complex.

Amino Acid Sequence↗
PubMed1992

Order and disorder in water structure of crystalline proteins.

Crystals of the hydrophobic protein, crambin (MW 4700), diffract to 0.83 A resolution at 130K. At this level of detail, nearly all the solvent molecules are ordered. Thus, this protein provides an excellent opportunity to study the order and disorder of water molecules at the protein surface. Water is important in stabilizing the folded conformation of the protein and also is necessary for enzymes to be active. In crambin, there are two types of water networks: pentagonal rings associated with the hydrophobic surface chain and chains linking the polar residues. The chain-like arrays appear to be strongly influenced by the protein surface. Study of these networks may enable us to predict the solvent shell in other proteins. The precise influence of the protein atoms on the solvent structure can be deduced by superimposing identical side chain functional groups and comparing the positions of atoms hydrogen-bonded to these reference atoms. Preliminary results with crambin indicate that there is different ordering of the solvent water molecules depending on whether the hydrogen-bonding protein molecule is greater than NH or greater than C = 0. Around -OH groups, the geometry of hydrogen-bonding is even more diverse. Two disordered water oxygen networks are located in each of the four major solvent regions of the crystal. Each alternate network may represent the necessity of water to pack against an irregular surface and still maximize hydrogen bonding. In the context of nature's balance between making strong bonds and maximizing disorder, the presence of disorder in the solvent structure of crambin is not unexpected. Free energy is the sum of bond energy (enthalpy) and disorder (entropy). However, considerable insight is gained from observing where disorder is and is not found in crystals of crambin.

Crystallization↗
PubMed1990

Crystal structure of a protein-toxin alpha 1-purothionin at 2.5A and a comparison with predicted models.

Alpha 1-Purothionin (alpha 1-P), a wheatgerm protein and lytic toxin, has a secondary and tertiary structure similar to that of crambin as revealed by CD and NMR studies. alpha 1-P crystallizes in the tetragonal space group 1422 with unit cell dimensions: a = b = 53.59 and c = 69.79 A. X-ray diffraction data have been measured to 2.5 A Bragg spacing. The crystal structure has been determined by molecular replacement methods, using an energy-minimized alpha 1-P model structure derived from crambin (Whitlow and Teeter: Journal of Biomolecular Structure and Dynamics 2:831-848, 1985, Journal of the American Chemical Society 108:7163-7172, 1986). The energy-minimized model gives a slightly cleaner rotation solution and better refinement against the x-ray data than do the crambin or unminimized alpha 1-P structures. The final crystallographic residual with the data in the 10-2.5 A resolution range is 0.216. The refined alpha 1-P structure has a backbone rms difference of 0.74 A from crambin and 0.55 A from the energy-minimized alpha 1-P model. A low resolution NMR model of alpha 1-P calculated from metric matrix distance geometry and restrained molecular dynamics differs from crambin's backbone by 2.3 A rms deviation (Clore et al.: EMBO Journal 5:2729-2735, 1986). Backbone dihedral angles for our predicted model differ from the refined alpha 1-P structure in only one region (at a turn where there is a deletion relative to crambin). The NMR model had differences in four regions.

Antimicrobial Cationic Peptides↗
PubMed1988

Test of circular dichroism (CD) methods for crambin and CD-assisted secondary structure prediction of its homologous toxins.

Methods that analyze protein circular dichroism (CD) spectra for fractions of secondary structure are evaluated for the plant protein crambin, which has a known high-resolution crystal structure. In addition, a two-step secondary structure prediction scheme is presented and used for the toxins homologous to crambin, shown by others to have secondary structures similar to crambin. The test of CD spectral analysis methods with the protein crambin employed two computer programs and several CD basis sets. Crambin's crystal structure, known to 0.945A resolution (Hendrickson, W.A., Teeter, M.M. Nature 290:107-113, 1981), allows accurate evaluation of results. Analysis with the protein spectra basis sets (Provencher, S.W., Glöckner, J. Biochemistry 20:33-37, 1981) as modified (Manavalan, P., Johnson, W.C., Jr. Anal. Biochem. 167:76-85, 1987) agreed most closely with crambin's crystal structure. This method was then applied to the CD spectra of the membrane-active toxins homologous to crambin (alpha 1- and beta-purothionin, phoratoxin A and B, and viscotoxin A3 and B). The new program SEQ (pronounced "seek") was developed to assign the secondary structure along the protein chain in a hierarchical fashion and applied to the plant toxins. The method constrained the secondary structure fractions to those from CD analysis and combined standard statistical methods with amphipathic helix location. Both CD-arrived secondary structure percentages and sequence assignment indicate that the viscotoxins are structurally most similar to crambin. Purothionin's secondary structure was predicted to be fundamentally similar to crambin's with a difference at the start of the first helix. This assignment agreed with Raman and NMR analyses of purothionin and lends validity to the method presented here. Differences from the NMR in the CD secondary structure fraction analysis for phoratoxin suggest interference in the CD from tryptophan residues.

Amino Acid Sequence↗
PubMed1988

Mapping the binding site of aflatoxin B1 in DNA: molecular modeling of the binding sites for the N(7)-guanine adduct of aflatoxin B1 in different DNA sequences.

Aflatoxin B1 (AFB1), a potent mutagen and carcinogen, forms an adduct exclusively at the N(7) position of guanine, but the structure of this adduct in double stranded DNA is not known. Molecular modeling (using the program, PSFRODO) in conjunction with molecular mechanical calculation (using the program, AMBER) are used to assess the binding modes available to this AFB1 adduct. Two modes appear reasonable; in one the AFB1 moiety is intercalated between the base pair containing the adducted guanine and the adjacent base pair on the 5'-side in reference to the adducted guanine, while in the second it is bound externally in the major groove of DNA. Rotational flexibility appears feasible in the latter providing four, potential binding sites. Molecular modeling reveals that the binding sites around the reactive guanine in different sequences are not uniformly compatible for interaction with AFB1. As the sequence is changed, one particular external binding site would be expected to give a pattern of reactivities that is reasonably consistent with the observed sequence specificity of binding that AFB1 shows in its reaction with DNA (Benasutti, M., Ejadi, S., Whitlow, M. D. and Loechler, E. L. (1988) Biochemistry 27, 472-481). The AFB1 moiety is face-stacked in the major groove with its long axis approximately perpendicular to the helix axis. Favorable interactions are formed between exocyclic amino groups that project into the major groove on cytosines and adenines surrounding the reactive guanine, and oxygens in AFB1; unfavorable interactions involve van der Waals contacts between the methyl group on thymine and the AFB1 moiety. "Some of the sequence specificity of binding data can be rationalized more readily if it is assumed that 5'-GG-3' sequences adopt an A-DNA structure." Based upon molecular modeling/potential energy minimization calculation, it is difficult to predict how reactivity would change in different DNA sequences in the case of the intercalative binding mode; however, several arguments suggest that intercalation might not be favored. From these considerations a model of the structure for the transition state in reaction of AFB1 with DNA is proposed involving one particular external binding site.

Aflatoxin B1↗
PubMed1987

Nuclear magnetic resonance study of the solution structure of alpha 1-purothionin. Sequential resonance assignment, secondary structure and low resolution tertiary structure.

The solution structure of the 45-residue plant protein, alpha 1-purothionin, is investigated by nuclear magnetic resonance (n.m.r.) spectroscopy. Using a combination of two-dimensional n.m.r. techniques to demonstrate through-bond and through-space (less than 5 A) connectivities, the 1H n.m.r. spectrum of alpha 1-purothionin is assigned in a sequential manner. The secondary structure elements are then delineated on the basis of a qualitative interpretation of short-range nuclear Overhauser effects (NOE) involving the NH, C alpha H and C beta H protons. There are two helices extending from residues 10 to 19 and 23 to 28, two short beta-strands from residues 3 to 5 and 31 to 34 which form a mini anti-parallel beta-sheet, and five turns. In addition, a number of long-range NOE connectivities are assigned and a low resolution tertiary structure is proposed.

Amino Acid Sequence↗
PubMed1987

A-DNA accommodates adducts derived from diol epoxides of polycyclic aromatic hydrocarbons bound in a "side-stacking" mode.

The minor groove of undistorted A-DNA provides a good binding site for planar, hydrophobic moieties such as unmetabolized polycyclic aromatic hydrocarbons (PAHs), and the base pairs at the ends of short oligodeoxynucleotide helices. It also accommodates the chief adduct derived from the metabolically activated form of the carcinogen benzo[a]pyrene. B-DNA lacks such a site. Computerized models have been generated for the major (N2-guanine-linked) adducts formed at this site by both + and - enantiomers of anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (anti-BPDE) with poly(dG).poly(dC) in the A-DNA conformation. The BPDE adducts lie in the shallow, relatively hydrophobic minor groove of the A-DNA after empirical potential energy minimization using the program AMBER. We term this binding mode "side-stacking." The side-stacked + anti-BPDE may constitute the chief carcinogenic lesion derived from benzo[a]pyrene.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗
PubMed1985

Energy minimization for tertiary structure prediction of homologous proteins: alpha 1-purothionin and viscotoxin A3 models from crambin.

Homologous proteins may fold into similar three-dimensional structures. Spectroscopic evidence suggests this is true for the cereal grain thionins, the mistletoe toxins, and for crambin, three classes of plant proteins. We have combined primary sequence homology and energy minimization to predict the structures alpha 1-purothionin (from Durum wheat) and viscotoxin A3 (from Viscum album, European mistletoe) from the high resolution (0.945 A) crystal structure of crambin (from Crambe abyssinica). Our predictions will be verifiable because we have diffraction-quality crystals of alpha 1-purothionin whose structure we are have predicted. The potential energy minimizations for each protein were performed both with and without harmonic constraints to its initial backbone to explore the existence of local minima for the predicted proteins. Crambin was run as a control to examine the effects of the potential energy minimization on a protein with a well-known structure. Only alpha 1-purothionin which has one fewer residue in a turn region shows a significant difference for the two minimization paths. The results of these predictions suggest that alpha 1-purothionin and viscotoxin are amphipathic proteins, and this character may relate to the mechanism of action for these proteins. Both are mildly membrane-active and their amphipatic character is well suited for interaction with a lipid bilayer.

Amino Acid Sequence↗
PubMed1984

Raman spectroscopy of homologous plant toxins: crambin and alpha 1- and beta-purothionin secondary structures, disulfide conformation, and tyrosine environment.

The Raman spectrum of crambin crystals is different from the spectrum of crambin in solution. The amide I spectrum of crambin in solution is not different from the solution spectra of proteins homologous (greater than 40%) with crambin, alpha 1- and beta-purothionins. We have two interpretations of these results. One is that helical segments in crambin and the purothionins in solution are more irregular than those in crystalline crambin. Comparative analyses of amide I and amide III spectra, and of the conformational preferences of the amino acid sequences of these proteins, are consistent with this interpretation. The other is that, due to the way helical segments in crambin are stacked end on end along the same axis in the crystal, transition dipole coupling along the axis of these extended helixes enhances the amide I intensity of helical residues. On the basis of a combined Raman and sequence conformational analysis, we propose that the structure of the purothionins is the same as that of crambin in solution and that residues 7-12 in crystalline crambin are somewhat more regular and ordered than they are in solutions.

Antimicrobial Cationic Peptides↗
PubMed1984

Water structure of a hydrophobic protein at atomic resolution: Pentagon rings of water molecules in crystals of crambin.

The water structure has been analyzed for a model of the protein crambin refined against 0.945-A x-ray diffraction data. Crystals contain 32% solvent by volume, and 77% of the solvent molecules have been located-i.e., 2 ethanol molecules and 64 water molecules with 10-14 alternate positions. Many water oxygen atoms found form chains between polar groups on the surface of the protein. However, a cluster of pentagonal arrays made up of 16 water molecules sits at a hydrophobic, intermolecular cleft and forms a cap around the methyl group of leucine-18. Several waters in the cluster are hydrogen-bonded directly to the protein. Additional closed circular arrays, which include both protein atoms and other water oxygen atoms, form next to the central cluster. This water array stretches in the b lattice direction between groups of three ionic side chains.

Journal Article↗
PubMed1984

Crambin in phospholipid vesicles: Circular dichroism analysis of crystal structure relevance.

Crambin, a hydrophobic plant seed protein that exhibits sequence homology to membrane-active plant toxins, was incorporated into phospholipid vesicles. Circular dichroism spectroscopy indicates that its structure in vesicles is nearly identical to its structure in 60% ethanol solution, the solvent from which the protein was crystallized. The secondary structure predicted from the circular dichroism data of the ethanol solution closely resembles that determined by x-ray diffraction of the crystals. This agreement suggests that the x-ray structure may form a useful basis for modeling the structure and behavior of lipophilic plant toxins. Finally, because the structure of crambin has been determined in an organic solvent medium, it provides a protein standard for examination of the effect of solvent dipole moment on the circular dichroism spectra of proteins, which may be important for interpretation of data for membrane proteins.

Journal Article↗
PubMed1981

Primary structure of the hydrophobic plant protein crambin.

Crambin, a hydrophobic plant seed protein, consists of a single chain of 46 amino acids with a calculated molecular weight of 4720. The primary structure was determined by using solid-phase sequencing techniques and was confirmed through X-ray crystallographic analysis of the protein at 1.5-A resolution [Hendrickson, W. A., & Teeter, M. M. (1981) Nature (London) 290, 107-112]. High-performance liquid chromatographic separation of the proteolytic fragments from crambin led to the identification of two sites of microheterogeneity. The three disulfide bonds were located at positions 3-40, 4-32, and 16-26 from the crystallographic data. Comparison of the primary structure with known sequences revealed that crambin is homologous with the plant toxins purothionin and viscotoxin. Methods to estimate protein secondary structure were applied and found to predict all of crambin's structure except its amphiphilic helix.

Amino Acid Sequence↗
PubMed1978

Structural analysis of spermine and magnesium ion binding to yeast phenylalanine transfer RNA.

Refinement of the diffraction data at 2.5-A resolution from orthorhombic crystals of yeast tRNAPhe has proceeded to the point where spermine and magnesium ions can be located in the difference electron density map. Two spermine molecules are found: one is located in the major groove at one end of the anticodon stem; the other is near the variable loop and curls around phosphate 10 in a region where the polynucleotide chain takes a sharp turn. Four distinct magnesium ions have been identified: one in the anticodon loop, two in the D loop, and one coordinated with phosphates 8, 9, 11, and 12, where the polynucleotide chain is coiled. The conformation of the anticodon stem and loop is stabilized by the cations at the end of the molecule. The positions of these ions may be related to aspects of the biological activity of tRNA. The spermine and magnesium ions appear to be important in maintaining the overall folding of the tRNA molecule.

Anticodon↗