Understanding covalent modifications of proteins by lipids: where cell biology and biophysics mingle.

Much effort has been expended on the in vitro characterization of enzymes that covalently attach lipids to proteins. Less information is available about properties conferred on modified proteins by their attached lipid groups, but biophysical studies of simple model systems have begun to shed light on this issue. Recent evidence suggests that the specificity of lipid modifications may be dependent upon the intracellular compartmentalization of the lipid and protein substrates of lipidating enzymes. The function and targeting of their lipidated products appear to be regulated dynamically through addition or subtraction of lipid moieties, other covalent or noncovalent modifications, as well as several devices that at this point can only be inferred. This field of research illustrates the necessity of integrating cell-biological and biophysical perspectives.

Intracellular pool of unhydroxylated polypeptide precursors of collagen.

The hydroxyproline and hydroxylysine in collagen are synthesized by an apparently unique pathway in which proline and lysine are hydroxylated after they are incorporated into a large polypeptide precursor of collagen called protocollagen. When the hydroxylation of protocollagen in isolated tissues is intermittently interrupted, hydroxylation can occur after complete polypeptides are released from ribosomal complexes. Cartilage from chick embryos was incubated with the iron chelator alpha,alpha'-dipyridyl for 2 hours to inhibit protocollagen hydroxylase, and then the inhibition was reversed by transferring the tissues to medium containing ferrous iron and no alpha,alpha'-dipyridyl. "Pulse labeling" of the tissues during these two periods indicated that both the accumulated protocollagen and the polypeptides synthesized after reversal of the inhibition were hydroxylated at the same rate. Even when no measures are taken to inhibit the hydroxylation of protocollagen, most of the hydroxyproline in collagen is probably synthesized after complete protocollagen polypeptides are released from ribosomes.

Loss of ability to synthesize collagen in fibroblasts transformed by rous sarcoma virus.

Transformation of chick embryo fibroblasts by Rous sarcoma virus inhibited their ability to synthesize collagen. Kinetic experiments showed that 72 hours after infection, collagen synthesis was reduced by 90%. Nontransforming Rous-associated viruses did not inhibit collagen synthesis. The inhibition resulted from the failure of the cells to synthesize collagen polypeptides rather than from a decrease in the activity of prolyl hydroxylase; the levels of prolyl hydroxylase were fourfold those in uninfected cells. The addition of dibutyryl cyclic AMP and theophylline, alone or together, did not restore collagen synthesis.

Inhibition of hydroxyproline synthesis by palladium ions.

Palladium ions, administered as PdSO4, markedly affect the incorporation of L-[3,4-3H2] proline into non-dialyzable fractions in 10-day chick embryo cartilage explants with a 55-65% reduction in the concentration range 0.06-0.6 mM. Under these conditions the synthesis of [3H]hydroxyproline was nearly completely inhibited. Experiments with prolyl hydroxylase (EC 1.14.11.2) indicated a strong irreversible inhibition of the enzyme with a competition between Fe2+ and Pd2+. The Ki for the inhibition was 0.02 mM. Pd2+-treated enzyme remained inactive after extensive dialysis. These studies suggest that Pd2+ may inhibit collagen synthesis by replacing Fe2+ in the active site of prolyl hydroxylase and forming strong complexes with the enzyme. These studies also point to a potential mechanism of Pd2+ toxicity.

The structure of myristoyl-CoA:protein N-myristoyltransferase.

Protein N-myristoylation is a covalent modification that occurs co-translationally in eukaryotes. Myristate, a rare 14 carbon saturated fatty acid (C14:0), is attached, via an amide linkage, to the N-terminal glycine of a subset of eukaryotic and viral proteins by myristoyl-CoA:protein N-myristoyltransferase (Nmt). Genetic and biochemical studies have established that Nmt is a target for development of a new class of fungicidal drugs. The enzyme is also a potential target for development of antiviral and antineoplastic agents. The structure of Saccharomyces cerevisiae Nmt1p has been determined recently with bound substrate analogs. The Nmt fold resembles the fold of members of the GCN5-related N-acetyltransferase superfamily. The structure reveals how Nmt's myristoyl-CoA and peptide substrates are recognized and bound, and what elements control the enzyme's ordered kinetic mechanism. Acyl transfer occurs through the nucleophilic addition-elimination reaction: an oxyanion hole formed by main chain atoms polarizes the thioester carbonyl and stabilizes the transition state while deprotonation of the ammonium of the Gly acceptor appears to be mediated by Nmt's C-terminal carboxylate. The use of main chain carboxylate atoms as general base catalyst is a novel feature.

Design of biomimetic habitats for tissue engineering with P-15, a synthetic peptide analogue of collagen.

In tissues, collagen forms the scaffold for cell attachment and migration, and it modulates cell differentiation and morphogenesis by mediating the flux of chemical and mechanical stimuli. We are constructing biomimetic environments by immobilizing a collagen-derived high-affinity cell-binding peptide P-15 in three-dimensional (3-D) templates. The cell-binding peptide can be expected to transduce mechanical forces. In their physiological environment, periodontal ligament fibroblasts (PDLF) are subject to significant mechanical forces. We have examined the behavior of human PDLF in culture on particulate bovine anorganic bone mineral (ABM) coated with P-15 (ABM-P-15). Greater numbers of cells associated with ABM-P-15 compared to ABM alone. Higher levels of incorporation of radiolabeled precursors in DNA and protein were consistent with the presence of larger numbers of cells on ABM-P-15 compared to ABM cultures. Scanning electron microscopic examination showed that cultures on ABM-P-15 generated highly oriented 3-D colonies of elongated cells and formed copious amounts of fibrous as well as membranous matrix reminiscent of ligamentous structures. PDLF cultured on ABM formed sparse monolayers with little order and a meager matrix. Alizarin Red stained the matrix of particle associated cells and inter-particle cellular bridges in P-15-associated cultures, indicating mineralization. 3-D colony formation and ordering of cells along with increased mineralization suggests that the coupling of cells to the ABM matrix through P-15 may provide a biomimetic environment permissive for cell differentiation and morphogenesis. Our studies suggest that ABM-P-15 templates may be effective as endosseous grafts, and, when seeded with PDLF, these matrices may serve as tissue engineered substitutes for autologous bone grafts.

Increased aryl hydrocarbon hydroxylase and prolyl hydroxylase activities in lung organ cultures exposed to benzo[a]pyrene.

Exposure of neo-natal rat lungs in organ culture to 10--25 microM benzo[a]pyrene (BaP) elevated the activities of aryl hydrocarbon hydroxylase (AHH) and prolyl hydroxylase (PH). Pyrene, a non-carcinogenic hydrocarbon did not elicit this response. Prolyl hydroxylase is an indicator of collagen synthesis and increased PH activity in the lungs reflects increased collagen synthesis. Our studies suggest that the earliest events in BaP-induced lung injury may include altered collagen metabolism.

Differential stability of the triple helix of (Pro-Pro-Gly)10 in H2O and D2O: thermodynamic and structural explanations.

(Pro-Pro-Gly)10 [(PPG10)], a collagen-like polypeptide, forms a triple-helical, polyproline-II structure in aqueous solution at temperatures somewhat lower than physiological, with a melting temperature of 24.5 degrees C. In this article, we present circular dichroism spectra that demonstrate an increase of the melting temperature with the addition of increasing amounts of D2O to an H2O solution of (PPG)10, with the melting temperature reaching 40 degrees C in pure D2O. A thermodynamic analysis of the data demonstrates that this result is due to an increasing enthalpy of unfolding in D2O vs. H2O. To provide a theoretical explanation for this result, we have used a model for hydration of (PPG)10 that we developed previously, in which inter-chain water bridges are formed between sterically crowded waters and peptide bond carbonyls. Energy minimizations were performed upon this model using hydrogen bond parameters for water, and altered hydrogen bond parameters that reproduced the differences in carbonyl oxygen-water oxygen distances found in small-molecule crystal structures containing oxygen-oxygen hydrogen bonds between organic molecules and H2O or D2O. It was found that using hydrogen bond parameters that reproduced the distance typical of hydrogen bonds to D2O resulted in a significant lowering of the potential energy of hydrated (PPG)10. This lowering of the energy involved energetic terms that were only indirectly related to the altered hydrogen bond parameters, and were therefore not artifactual; the intra-(PPG10) energy, plus the water-(PPG10) van der Waals energy (not including hydrogen bond interactions), were lowered enough to qualitatively account for the lower enthalpy of the triple-helical conformation, relative to the unfolded state, in D2O vs. H2O. This result indicates that the geometry of the carbonyl-D2O hydrogen bonds allows formation of good hydrogen bonds without making as much of an energetic sacrifice from other factors as in the case of hydration by H2O.

The role in cell binding of a beta-bend within the triple helical region in collagen alpha 1 (I) chain: structural and biological evidence for conformational tautomerism on fiber surface.

In its physiological solid state, type I collagen serves as a host for many types of cells. Only the molecules on fiber surface are available for interaction. In this interfacial environment, the conformation of a cell binding domain can be expected to fluctuate between the collagen fold and a distinctive non-collagen molecular marker for recognition and allosteric binding. If the cell binding domain can be localized in contiguous residues within the exposed half of a turn of the triple helix (approximately 15 residues), the need for extensive structural modification and unraveling of the triple helix is avoided. We examined the conformational preferences and biological activity of a synthetic 15-residue peptide (P-15), analogous to the sequence 766GTPGPQGIAGQRGVV780 in the alpha 1 (I) chain. Theoretical studies showed a high potential for a stable beta-bend for the central GIAG sequence. The flanking sequences showed facile transition to extended conformations. Circular dichroism of the synthetic peptide in anisotropic solvents confirmed the presence of beta-strand and beta-bend structures. P-15 inhibited fibroblast binding to collagen in a concentration dependent manner, with near maximal inhibition occurring at a concentration of 7.2 x 10(-6) M. The temporal pattern of cell attachment was altered markedly in the presence of P-15. No inhibition was seen with a peptide P-15(AI), an analogue of P-15 with the central IA residues reversed to AI or with collagen-related peptides (Pro-Pro-Gly)10, (Pro-Hyp-Gly)10, and polyproline, and with several unrelated peptides. Our studies suggest a molecular mechanism for cell binding to collagen fibers based on a conformational transition in collagen molecules on the fiber surface. Since the energy barrier between the collagen fold and beta-strand conformation is low, a local conformational change may be possible in molecules on the fiber surface because of their location in an anisotropic environment. Our observations also suggest that the sequence incorporated in P-15 may be a specific ligand for cells. Unlike other reported cell binding peptides, the residues involved in this interaction are non-polar.

The role of bound water in the stability of the triple-helical conformation of (Pro-Pro-Gly)10.

There is significant experimental evidence for bound water in collagen and related polymers. (Pro-Pro-Gly)10 [(PPG)10] is a polymer that forms a collagen-like triple-helical structure in aqueous solution. Like collagen, (PPG)10 adopts a structure in which side chains are mostly exposed to solvent, and the backbone polar groups are limited in their ability to form hydrogen bonds with each other. (PPG)10, like collagen, also has many of its backbone polar groups in positions that inhibit complete solvation in aqueous solution; thus the necessity of bound waters for stabilization of the structure. We have constructed a model for bound waters in (PPG)10, based on an examination of the geometry and steric environment of the backbone polar groups. As will become clear, the number of bound waters is determined by the geometry of the backbone carbonyl groups and the steric crowding surrounding them. In this model, each water forms one hydrogen bond with each of two backbone carbonyls from a glycine and a proline in different monomer chains, thus bridging the two carbonyls. The carbonyls in question are quite sterically crowded by neighboring (PPG)10 atoms and would not be likely to experience complete solvation by bulk solvent in aqueous solution. The bound waters are therefore likely to be present even in solution, since otherwise the unsatisfied hydrogen-bonding potential of the carbonyls would destabilize the structure. Other carbonyls also are sterically crowded and possibly prevented from experiencing full solvation, but are not in a favorable geometry for such bridging hydrogen bonds. The intra- and interchain interactions found in a previous computational study of (PPG)10 without bound waters are not disrupted by the addition of waters.

Inter-chain proline:proline contacts contribute to the stability of the triple helical conformation.

The triple helical conformation observed in the collagen group of proteins is related to the presence of large numbers of imino residues and is derived from the stereochemical properties of these residues. The triple helix is stabilized by increasing numbers of these residues. Hydrogen bonds are usually considered to be a major factor in the formation and stability of protein conformation, however, imino residues are not hydrogen bond donors. We have evaluated the role of these residues in stabilizing the triple helix by re-examining two X-ray based structures of the triple helical polypeptide (Pro-Pro-Gly)10 using molecular mechanics calculations. The two minimized structures are comparable in energy and have helical parameters close to the starting values for each starting structure. Our studies suggest that clusters of close van der Waals contacts between proline residues in adjacent chains contribute significantly to the stability of the triple helix. Preliminary NMR studies support this concept. We propose that non-bonded interactions between proline residues may be a significant stabilizing force in the triple helix generated by (Pro-Pro-Gly)10.

Creatine kinase and lactate dehydrogenase isoenzyme patterns in cultured normal and pathological gingival fibroblasts.

The isoenzyme patterns of creatine kinase (CK) and lactate dehydrogenase (LDH) were examined in cultured fibroblasts derived from the gingival tissue of a healthy person and patients with periodontitis and gingival fibromatosis. Human foreskin fibroblasts were also included for comparison. Cytosol fractions were prepared by sonication and centrifugation. Gingival fibroblasts from normal subjects (A), and from patients with periodontitis (B) or fibromatosis (C), exhibited CK-MM (muscle form) as a predominant isoenzyme and CK-BB (brain form) as a minor fraction. There was no significant difference in specific activities of CK-BB fraction in all 3 types of fibroblasts. However, B fibroblasts contained a higher proportion of MM type isoenzyme than A fibroblasts. C fibroblasts showed the lowest amount of CK-MM isoenzyme as compared to either A or B fibroblasts. In contrast, fibroblasts derived from human foreskin (D) contained only a small amount of CK-BB isoenzyme, but CK-MM was not present. In the studies of LDH isoenzymes, A, B, and C fibroblasts possessed only 3 isoenzymes, namely, LDH-3, LDH-4 and LDH-5. In terms of the relative abundance of M vs H subunits, A, B, and C fibroblasts were shown to have a preponderance of M subunits (85-87% M vs 13-15% H subunits). In comparison, D fibroblasts contained 4 isoenzymes (LDH-2, LDH-3, LDH4, LDH-5) with 73% M and 27% H subunits. The ratio of LDH-5 to LDH-4 was calculated for all fibroblasts tested, and the values were 1.11 in A, 1.39 in B, 1.16 in C and 0.64 in D.(ABSTRACT TRUNCATED AT 250 WORDS)

Fibroblasts derived from tissue explants of dilantin-induced gingival hyperplasia and idiopathic gingival fibromatosis show distinct disparity in proliferative responsiveness to epidermal growth factor.

Human gingival fibroblasts derived from tissue explants of two patients with dilantin-induced gingival hyperplasia (DGH) and one patient with idiopathic gingival fibromatosis (GF) were studied with respect to the effect of epidermal growth factor (EGF) on the proliferative characteristics of these cells. Immunohistochemical staining showed that there were more EGF receptor-positive cells among DGH fibroblasts than among either normal gingival fibroblasts (NG) or GF cells. Furthermore, EGF binding studies showed that, in spite of there being no disparity in binding affinity among all these cells, DGH fibroblasts possessed approximately two-fold more EGF receptors than either NG or GF cells. In addition, the growth-promoting effect of exogenously added EGF was concentration-dependent in DGH fibroblasts but was not in either NG or GF cells. All of the above findings clearly demonstrate that DGH and GF fibroblasts exhibit distinct disparity in proliferative responsiveness to EGF and suggest that different mechanisms may be involved in the pathogenesis of these two forms of gingival hyperplasia. These observations also suggest a possible therapeutic approach for blocking EGF-induced cell proliferation in DGH.

Cytomodulin-1, a synthetic peptide abrogates oncogenic signaling pathways to impede invasion and angiogenesis in the hamster cheek pouch carcinogenesis model.

Constitutive activation of the various oncogenic signaling pathways plays a pivotal role in promoting malignant transformation. The aim of this study was to investigate the therapeutic potential of a synthetic bioactive heptapeptide cytomodulin-1 (CM-1) against hamster cheek pouch carcinomas based on its influence on the predominant carcinogenic signaling pathways - NF-κB, TGFß, and Wnt/ß-catenin and their downstream target events invasion and angiogenesis. Topical application of CM-1 to DMBA-painted hamsters significantly inhibited activation of the canonical NF-κB pathway by blocking kinase activity of IKKß and increasing the cytosolic accumulation of the inhibitor IκB-α. In addition, CM-1 inactivated IKKß by disrupting IKKß/Nemo interactions. CM-1 also hampered the activation of TGFß and Wnt/ß-catenin signaling by averting the phosphorylation of the key upstream ser/thr kinases TGFß RI and GSK-3ß respectively. Attenuation of these oncogenic signaling pathways by CM-1 also mitigated invasion and angiogenesis by suppressing the expression of pro-invasive matrix metalloproteinases, pro-angiogenic VEGF and HIF-1α and upregulating the anti-angiogenic TIMP-2. Synthetic peptides such as CM-1 that target multiple key molecules in oncogenic signaling pathways and their downstream events are ideal candidate agents for cancer chemotherapy.