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M H Zehfus

Publications and source records attributed to M H Zehfus.

15 recordsLinked to original sources
PubMed1998

Effects of backbone modification on helical peptides: the reduced carbonyl modification.

Reducing a CO to a CH2 moiety in a peptide bond destroys the ability of the peptide link to act as a proton acceptor in a hydrogen-bonded structure. Here, this modification is introduced into different positions of the helical peptide, acetyl-WGG(RAAAA)4R-amide, and the melting of these peptides is followed using CD. Effects of this modification on helical peptides are compared to our previous N-methylation studies [C. F. Chang and M. H. Zehfus (1996) Biopolymers, Vol. 40, pp. 609-616]. While the experiments were designed to remove the same hydrogen bond from the peptide, no consistent results are obtained between these two modifications. This result suggests that these modifications not only break the backbone hydrogen bonds, but also involve other destabilizing effects. When our data is analyzed using different helix-coil transition models, the results show that as the models increase in complexity the energy associated with a single residue modification increases. Unfortunately, the most detailed dichroic model, which should best describe this system, works for only one peptide. Apparently, the models need to be further improved to better mimic our system.

Amino Acid Sequence↗
PubMed1997

Identification of compact, hydrophobically stabilized domains and modules containing multiple peptide chains.

Compactness has been used to locate discontinuous structural units containing one or more polypeptide chains in proteins of known structure. Rather than exhaustively calculating the compactness of all possible units, our procedure uses a screening algorithm to find discontinuous regions that are potentially compact. Precise calculations of compactness are restricted only to units in these regions. With our procedure, compactness can be used to discover discontinuous domains with virtually any number of disjoint peptides. Small, single-domain proteins may contain several compact regions: thus, compact regions do not always correspond to folding domains. Because a domain is an independent folding unit and should contain a hydrophobic core, compact units were further examined for the presence of hydrophobic clusters (Zehfus MH, 1995, Protein Sci 4:1188-1202). This added constraint limits the number of acceptable units and helps greatly in the location of the true structural domains. The larger hydrophobically stabilized compact units correspond to domains, while the smaller units may correspond to folding intermediates.

Algorithms↗
PubMed1996

The effect of N-methylation on helical peptides.

In N-methyl amino acids, the hydrogen of the N-H group is replaced with a bulky methyl group. While this change is expected to destabilize helical structures, the amount of destabilization is not known. Here the N-methyl group is placed into several positions of the helical peptides, acetyl-WGG(EAAAR)4A-amide and acetyl-WGG(RAAAA)4R-amide, and the melting of the peptides followed using CD. When analyzed using a simple two-state model, the destabilization associated with the H to CH3 substitution at 0 degree C is between 0.3 to 1.7 kcal/mole and is position dependent. The melting data may also be analyzed using a modified form of the Lifson-Roig statistics that should more correctly model the helix-coil transition in this small peptide. This analysis fails, however, apparently because the destabilization energy is greater than the energy that can be attributed to a single residue in this model.

Amino Acid Sequence↗
PubMed1995

Structure of a compact peptide from staphylococcal nuclease determined by circular dichroism and NMR spectroscopy.

Compact regions in proteins are thought to correspond to domains. If this is true, the structure of a compact region excised from a protein should closely resemble the structure in the intact protein. To test this theory, a compact peptide corresponding to residues 129-142 of staphylococcal nuclease (Ac-EAQAKKEKLNIWS-NH2) was synthesized and its solution structure determined using circular dichroism (CD) and 2D NMR. In aqueous solution, the peptide exhibits CD spectra characteristic of a nascent helix. This nascent helical structure is stabilized by the addition of 2,2,2-trifluoroethanol. Under these conditions, the chemical shift indexes of the 1H alpha and 13C alpha resonances, temperature coefficients of amide protons, and NOE constraints are all consistent with the peptide's structure being a helix-turn. This structure is almost identical to that found in the intact protein.

Amino Acid Sequence↗
PubMed1995

Automatic recognition of hydrophobic clusters and their correlation with protein folding units.

A method is described to objectively identify hydrophobic clusters in proteins of known structure. Clusters are found by examining a protein for compact groupings of side chains. Compact clusters contain seven or more residues, have an average of 65% hydrophobic residues, and usually occur in protein interiors. Although smaller clusters contain only side-chain moieties, larger clusters enclose significant portions of the peptide backbone in regular secondary structure. These clusters agree well with hydrophobic regions assigned by more intuitive methods and many larger clusters correlate with protein domains. These results are in striking contrast with the clustering algorithm of J. Heringa and P. Argos (1991, J Mol Biol 220:151-171). That method finds that clusters located on a protein's surface are not especially hydrophobic and average only 3-4 residues in size. Hydrophobic clusters can be correlated with experimental evidence on early folding intermediates. This correlation is optimized when clusters with less than nine hydrophobic residues are removed from the data set. This suggests that hydrophobic clusters are important in the folding process only if they have enough hydrophobic residues.

Algorithms↗
PubMed1994

Binary discontinuous compact protein domains.

Few methods exist that identify discontinuous protein domains containing more than one polypeptide chain. This paper describes a new method for locating such discontinuous domains based on their compactness, and applies the methodology to locate the most compact domains in bovine pancreatic trypsin inhibitor, ribonuclease, cytochrome c and myoglobin. The compactness of all binary discontinuous peptide combinations is first exhaustively evaluated. Several screening steps are then used to locate those compact units that represent global minima of compactness. Since domains are generally taken to be large, mutually exclusive structures that span most of the protein's sequence, compact domains were found by examining all compact units (both continuous and discontinuous) to locate two or three units that span most of the protein's sequence, have little mutual overlap and good overall compactness. Compact domains compare well with domains found by other methods and with experimental evidence that may differentiate domain structure. The strongest experimental evidence for the existence of compact discontinuous domains comes from the work of Oas and Kim [(1988) Nature, 336, 42-48] where a peptide that corresponds almost exactly to a compact domain has been synthesized and shown to have native-like structure in solution.

Algorithms↗
PubMed1993

Improved calculations of compactness and a reevaluation of continuous compact units.

A new method for calculating compactness (Z) that uses look-up table-based algorithms for area and volume computations is introduced. These algorithms can be used in any iterative area or volume calculation, are more than 1000 times faster than the original algorithms, and have equal or better precision. With the faster algorithms it is now possible to calculate the compactness of all continuous units in a protein, and to precisely locate the optimal compact units without the screening functions and limited resolution used previously. These methods have been incorporated into a fully automatic domain finding algorithm, and this method has been applied to the 21 proteins originally analyzed as well as 12 additional proteins. This method is robust, and yields similar units even when applied to coordinates of protein crystals grown under different experimental conditions.

Alcohol Dehydrogenase↗
PubMed1990

1H, 13C, and 15N resonance assignments for a ferrocytochrome c553 heme by multinuclear NMR spectroscopy.

A novel strategy has been used to assign the 1H, 13C, and 15N resonances of the heme in Anabaena 7120 ferrocytochrome c553. 13C[13C] double-quantum coherence spectroscopy was used to delineate the heme carbons, 1H[13C] single-bond correlation spectroscopy was used to define the attached protons, and 1H[15N] multiple-bond correlation spectroscopy was used to assign the nitrogens. 1H[13C] multiple-bond correlation spectroscopy confirmed many of the assignments. Proteins were labeled uniformly with 13C or 15N to obtain the required spectral sensitivity.

Carbon Isotopes↗
PubMed1987

Continuous compact protein domains.

The coefficient of compactness was recently introduced and used to locate domains in lysozyme and ribonuclease (Zehfus and Rose: Biochemistry 25:5759-5765, 1986). Nineteen additional proteins now have been analyzed by using this measure. Complete listings of compact units and plots showing their hierarchic organization are presented for all twenty-one proteins. Large compact units correspond well to protein domains; however, many smaller compact structures of equal or better compactness are also found. Since small compact units could represent subdomains or protein-folding intermediates, their structural composition is further examined.

Biometry↗
PubMed1986

Compact units in proteins.

An explicit measure of geometric compactness called the coefficient of compactness is introduced. This single value figure of merit identifies those continuous segments of the polypeptide chain having the smallest solvent-accessible surface area for their volume. These segments are the most compact units of the protein, and the larger ones correspond to conventional protein domains. To demonstrate the plausibility of this approach as a method of identifying protein domains, the measure is applied to lysozyme and ribonuclease to discover their constituent compact units. These units are then compared with domains, subdomains, and modules found by other methods. To show the sensitivity of the method, the measure is used to successfully differentiate between native and deliberately misfolded proteins [Novotný, J., Bruccoleri, R., & Karplus, M. (1984) J. Mol. Biol. 177, 787-818]. Methods that utilize only backbone atoms to define domains cannot distinguish between authentic and misfolded molecules because their backbone conformations are virtually superimposable. Compact units identified by this method exhibit a hierarchic organization. Such an organization suggests possible folding pathways that can be tested experimentally.

Hemerythrin↗
PubMed1985

Hydrophobicity of amino acid residues in globular proteins.

During biosynthesis, a globular protein folds into a tight particle with an interior core that is shielded from the surrounding solvent. The hydrophobic effect is thought to play a key role in mediating this process: nonpolar residues expelled from water engender a molecular interior where they can be buried. Paradoxically, results of earlier quantitative analyses have suggested that the tendency for nonpolar residues to be buried within proteins is weak. However, such analyses merely classify residues as either "exposed" or "buried." In the experiment reported in this article proteins of known structure were used to measure the average area that each residue buries upon folding. This characteristic quantity, the average area buried, is correlated with residue hydrophobicity.

Amino Acids↗
PubMed1977

Radioactive components in the acid-soluble fraction of mouse liver cytosol after dimethylnitrosamine[methyl-14C] administration.

The acid-soluble components of mouse-liver cytosol, prepared at time intervals after intragastric administration of a single carcinogenic dose of 14C-dimethylnitrosamine, were separated by column chromatography. The columns were calibrated with known in vitro metabolites of the nitrosamine, and the elution profiles were compared with those of the mouse-liver system. The results suggest that the 14C-methyl label is transferred to many of the same compounds as identified in vitro, but that numerous other labeled compounds are also present. The possible significance of these metabolites to the pathogenic processes induced by dimethylnitrosamine has yet to be determined.

Acids↗