A preliminary three-dimensional structure of angiogenin

Characterization and Function of the Interaction of Angiogenin With Alpha-Actinin 2

Angiogenin (ANG) is the first human tumor-derived angiogenic protein, which can promote angiogenesis and tumor growth. In a previous study, we identified alpha-actinin 2 (ACTN2), a cytoskeletal protein, as a direct interacting protein with angiogenin. However, the interaction between ANG and ACTN2 was not characterized in detail, which may provide information on the molecular mechanisms of ANG functions. In this study, we mapped the accurate binding domain and sites in ANG and ACTN2, respectively. In ANG, the residues from 83 to 105 are the smallest motif that can bind to ACTN2. We then use site mutation analysis to identify the precise binding sites of ANG in the interaction and found that the 101st residue arginine (R101) represents the critical residue involved in the ANG–ACTN2 interaction. In ACTN2, the residues from 383 to 632, containing two spectrin domains in the middle of the rod structure of ACTN2, play an important role in the interaction. Furthermore, we validated the interaction of ACTN2-383–632 to ANG by glutathione-S-transferase (GST) pull-down assay. In functional analysis, overexpressed ACTN2-383–632 could impair tumor cell motility observably, including cell migration and invasion. Meanwhile, ACTN2-383–632 overexpression inhibited tumor cell proliferation and survival as well. These data suggest that an excess expression of ACTN2 segment ACTN2-383–632 can inhibit tumor cell motility and proliferation by interfering with the interaction between ANG and ACTN2, which provides a potential mechanism of ANG action in tumor growth and metastasis.

Three decades of research on angiogenin: a review and perspective

As a member of the vertebrate-specific secreted ribonucleases, angiogenin (ANG) was first isolated and identified solely by its ability to induce new blood vessel formation, and now, it has been recognized to play important roles in various physiological and pathological processes through regulating cell proliferation, survival, migration, invasion, and/or differentiation. ANG exhibits very weak ribonucleolytic activity that is critical for its biological functions, and exerts its functions through activating different signaling transduction pathways in different target cells. A series of recent studies have indicated that ANG contributes to cellular nucleic acid metabolism. Here, we comprehensively review the results of studies regarding the structure, mechanism, and function of ANG over the past three decades. Moreover, current problems and future research directions of ANG are discussed. The understanding of the function and mechanism of ANG in a wide context will help to better delineate its roles in diseases, especially in cancer and neurodegenerative diseases.

dissectHMMER: a HMMER-based score dissection framework that statistically evaluates fold-critical sequence segments for domain fold similarity

Background

Annotation transfer for function and structure within the sequence homology concept essentially requires protein sequence similarity for the secondary structural blocks forming the fold of a protein. A simplistic similarity approach in the case of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc.) is not justified and a pertinent source for mistaken homologies. The latter is either due to positional sequence conservation as a result of a very simple, physically induced pattern or integral sequence properties that are critical for function. Furthermore, against the backdrop that the number of well-studied proteins continues to grow at a slow rate, it necessitates for a search methodology to dive deeper into the sequence similarity space to connect the unknown sequences to the well-studied ones, albeit more distant, for biological function postulations.

Results

Based on our previous work of dissecting the hidden markov model (HMMER) based similarity score into fold-critical and the non-globular contributions to improve homology inference, we propose a framework-dissectHMMER, that identifies more fold-related domain hits from standard HMMER searches. Subsequent statistical stratification of the fold-related hits into cohorts of functionally-related domains allows for the function postulation of the query sequence. Briefly, the technical problems as to how to recognize non-globular parts in the domain model, resolve contradictory HMMER2/HMMER3 results and evaluate fold-related domain hits for homology, are addressed in this work. The framework is benchmarked against a set of SCOP-to-Pfam domain models. Despite being a sequence-to-profile method, dissectHMMER performs favorably against a profile-to-profile based method-HHsuite/HHsearch. Examples of function annotation using dissectHMMER, including the function discovery of an uncharacterized membrane protein Q9K8K1_BACHD (WP_010899149.1) as a lactose/H+ symporter, are presented. Finally, dissectHMMER webserver is made publicly available at http://dissecthmmer.bii.a-star.edu.sg.

Conclusions

The proposed framework-dissectHMMER, is faithful to the original inception of the sequence homology concept while improving upon the existing HMMER search tool through the rescue of statistically evaluated false-negative yet fold-related domain hits to the query sequence. Overall, this translates into an opportunity for any novel protein sequence to be functionally characterized.

Reviewers

This article was reviewed by Masanori Arita, Shamil Sunyaev and L. Aravind.

Electronic supplementary material

The online version of this article (doi:10.1186/s13062-015-0068-3) contains supplementary material, which is available to authorized users.

On the necessity of dissecting sequence similarity scores into segment-specific contributions for inferring protein homology, function prediction and annotation

Background

Protein sequence similarities to any types of non-globular segments (coiled coils, low complexity regions, transmembrane regions, long loops, etc. where either positional sequence conservation is the result of a very simple, physically induced pattern or rather integral sequence properties are critical) are pertinent sources for mistaken homologies. Regretfully, these considerations regularly escape attention in large-scale annotation studies since, often, there is no substitute to manual handling of these cases. Quantitative criteria are required to suppress events of function annotation transfer as a result of false homology assignments.

Results

The sequence homology concept is based on the similarity comparison between the structural elements, the basic building blocks for conferring the overall fold of a protein. We propose to dissect the total similarity score into fold-critical and other, remaining contributions and suggest that, for a valid homology statement, the fold-relevant score contribution should at least be significant on its own. As part of the article, we provide the DissectHMMER software program for dissecting HMMER2/3 scores into segment-specific contributions. We show that DissectHMMER reproduces HMMER2/3 scores with sufficient accuracy and that it is useful in automated decisions about homology for instructive sequence examples. To generalize the dissection concept for cases without 3D structural information, we find that a dissection based on alignment quality is an appropriate surrogate. The approach was applied to a large-scale study of SMART and PFAM domains in the space of seed sequences and in the space of UniProt/SwissProt.

Conclusions

Sequence similarity core dissection with regard to fold-critical and other contributions systematically suppresses false hits and, additionally, recovers previously obscured homology relationships such as the one between aquaporins and formate/nitrite transporters that, so far, was only supported by structure comparison.

Transmembrane helix: simple or complex

Transmembrane helical segments (TMs) can be classified into two groups of so-called ‘simple’ and ‘complex’ TMs. Whereas the first group represents mere hydrophobic anchors with an overrepresentation of aliphatic hydrophobic residues that are likely attributed to convergent evolution in many cases, the complex ones embody ancestral information and tend to have structural and functional roles beyond just membrane immersion. Hence, the sequence homology concept is not applicable on simple TMs. In practice, these simple TMs can attract statistically significant but evolutionarily unrelated hits during similarity searches (whether through BLAST- or HMM-based approaches). This is especially problematic for membrane proteins that contain both globular segments and TMs. As such, we have developed the transmembrane helix: simple or complex (TMSOC) webserver for the identification of simple and complex TMs. By masking simple TM segments in seed sequences prior to sequence similarity searches, the false-discovery rate decreases without sacrificing sensitivity. Therefore, TMSOC is a novel and necessary sequence analytic tool for both the experimentalists and the computational biology community working on membrane proteins. It is freely accessible at http://tmsoc.bii.a-star.edu.sg or available for download.

Not all transmembrane helices are born equal: Towards the extension of the sequence homology concept to membrane proteins

BACKGROUND

Sequence homology considerations widely used to transfer functional annotation to uncharacterized protein sequences require special precautions in the case of non-globular sequence segments including membrane-spanning stretches composed of non-polar residues. Simple, quantitative criteria are desirable for identifying transmembrane helices (TMs) that must be included into or should be excluded from start sequence segments in similarity searches aimed at finding distant homologues.

RESULTS

We found that there are two types of TMs in membrane-associated proteins. On the one hand, there are so-called simple TMs with elevated hydrophobicity, low sequence complexity and extraordinary enrichment in long aliphatic residues. They merely serve as membrane-anchoring device. In contrast, so-called complex TMs have lower hydrophobicity, higher sequence complexity and some functional residues. These TMs have additional roles besides membrane anchoring such as intra-membrane complex formation, ligand binding or a catalytic role. Simple and complex TMs can occur both in single- and multi-membrane-spanning proteins essentially in any type of topology. Whereas simple TMs have the potential to confuse searches for sequence homologues and to generate unrelated hits with seemingly convincing statistical significance, complex TMs contain essential evolutionary information.

CONCLUSION

For extending the homology concept onto membrane proteins, we provide a necessary quantitative criterion to distinguish simple TMs (and a sufficient criterion for complex TMs) in query sequences prior to their usage in homology searches based on assessment of hydrophobicity and sequence complexity of the TM sequence segments.

A historical perspective of template-based protein structure prediction

This chapter presents a broad and a historical overview of the problem of protein structure prediction. Different structure prediction methods, including homology modeling, fold recognition (FR)/protein threading, ab initio/de novo approaches, and hybrid techniques involving multiple types of approaches, are introduced in a historical context. The progress of the field as a whole, especially in the threading/FR area, as reflected by the CASP/CAFASP contests, is reviewed. At the end of the chapter, we discuss the challenging issues ahead in the field of protein structure prediction.

Evolution of physics-based methodology for exploring the conformational energy landscape of proteins

The evolution of our physics-based computational methods for determining protein conformation without the introduction of secondary-structure predictions, homology modeling, threading, or fragment coupling is described. Initial use of a hard-sphere potential captured much of the structural properties of polypeptide chains, and subsequent more refined force fields, together with efficient methods of global optimization provide indications that progress is being made toward an understanding of the interresidue interactions that underlie protein folding.

Evolution of plasminogen-related growth factors (HGF/SF and HGF1/MSP)

HGF/SF and HGF1/MSP define a novel growth factor family whose members share the domain structure and the proteolytic process of activation of the blood proteinase precursor plasminogen. The amino acid and RNA sequences of HGF/SF and HGF1/MSP, the intron-exon organization of their genes and the predicted 3D structure of individual domains indicate that HGF/SF and HGF1/MSP evolved along with plasminogen and other members of the kringle-serine proteinase (KSP) superfamily from an ancestral gene that contained a single copy of the kringle domain, a serine proteinase domain and an activation peptide connecting the two domains. A series of intragenic duplications of the kringle domain, gene duplications, exon shuffling and deletions is responsible for the genes currently present in mammals, avians and amphibians. Plasminogen, HGF/SF and HGF1/MSP represent paradigmatic examples of the modern, multi-domain proteins typically associated with vertebrate organisms and illustrate a novel evolutionary pathway that led to the emergence of molecules with growth regulatory activity from proteolytic enzymes.

Homology modeling using simulated annealing of restrained molecular dynamics and conformational search calculations with CONGEN: application in predicting the three-dimensional structure of murine homeodomain Msx-1

We have developed an automatic approach for homology modeling using restrained molecular dynamics and simulated annealing procedures, together with conformational search algorithms available in the molecular mechanics program CONGEN (Bruccoleri RE, Karplus M, 1987, Biopolymers 26:137-168). The accuracy of the method is validated by "predicting" structures of two homeodomain proteins with known three-dimensional structures, and then applied to predict the three-dimensional structure of the homeodomain of the murine Msx-1 transcription factor. Regions of the unknown protein structure that are highly homologous to the known template structure are constrained by "homology distance constraints," whereas the conformations of nonhomologous regions of the unknown protein are defined only by the potential energy function. A full energy function (excluding explicit solvent) is employed to ensure that the calculated structures have good conformational energies and are physically reasonable. As in NMR structure determinations, information on the consistency of the structure prediction is obtained by superposition of the resulting family of protein structures. In this paper, our homology modeling algorithm is described and compared with related homology modeling methods using spatial constraints derived from the structures of homologous proteins. The software is then used to predict the DNA-bound structures of three homeodomain proteins from the X-ray crystal structure of the engrailed homeodomain protein (Kissinger CR et al., 1990, Cell 63:579-590). The resulting backbone and side-chain conformations of the modeled yeast Mat alpha 2 and D. melanogaster Antennapedia homeodomains are excellent matches to the corresponding published X-ray crystal (Wolberger C et al., 1991, Cell 67:517-528) and NMR (Billeter M et al., 1993, J Mol Biol 234:1084-1097) structures, respectively. Examination of these structures of Msx-1 reveals a network of highly conserved surface salt bridges that are proposed to play a role in regulating protein-protein interactions of homeodomains in transcription complexes.

A comparison of the predicted and X-ray structures of angiogenin. Implications for further studies of model building of homologous proteins

The three-dimensional structure of human angiogenin has been determined by X-ray crystallography and is compared here with an earlier model which predicted its structure, based on the homology of angiogenin with bovine pancreatic ribonuclease A. Comparison of the predicted model and crystal structure shows that the active-site histidine residues and the core of the angiogenin molecule, including most of the beta-strands and alpha-helices, were predicted reasonably well. However, the structure of the surface loop regions and residues near the truncated C-terminus differs significantly. The C-terminal segment includes the active-site residues Asp-116, Gln-117, and Ser-118; Gln-117 in particular has been shown to be important in affecting the ribonucleolytic activity of angiogenin. Also, the orientation of one helix in the model differed from the orientation observed experimentally by about 20 degrees, resulting in a large displacement of this chain segment. The difficulty encountered in predicting the surface loop regions has led to a new algorithm [Palmer and Scheraga (1991), J. Comput. Chem., 12, 505-526; (1992), J. Comput. Chem., 13, 329-350] for predicting the conformations of surface loops.

Proton resonance assignments and secondary structure of bovine angiogenin

Angiogenins are 14-kDa proteins able to induce blood vessel growth in various preparations and are thus thought to be involved in the development of solid tumors. Angiogenins have significant similarities with extracellular ribonuclease and possess a characteristic nuclease activity against large RNA molecules. These proteins are also able to induce second-messenger pathways. We have undertaken the determination of the three-dimensional structure of bovine angiogenin by using nuclear magnetic resonance (NMR) spectroscopy. Since this protein was directly purified from cow milk, it was not possible to enrich angiogenin with 13C or 15N isotopes. However, extensive use of two-dimensional and three-dimensional proton NMR experiments enabled us to identify all but four spin systems and to assign all corresponding proton resonances. Identification of most backbone-backbone nuclear Overhauser enhancements led to the characterization of the secondary structure elements of the protein. Comparison with the structure of ribonuclease A and analysis of the location of conserved residues confirmed that the two molecules have very similar structures.

Design of potential angiogenin inhibitors

A model of angiogenin has been prepared by homology modelling, based upon the structure of ribonuclease A. This model has been used to postulate an inhibitor based upon the angiostatic agent TAN1120. The complex of ribonuclease A with a dinucleotide has been modelled and used as a guide to the binding orientation of daunomycin--the closest TAN1120 analogue for which the crystal structure and stereochemistry are available.

Crystal structure of human angiogenin reveals the structural basis for its functional divergence from ribonuclease

Angiogenin, a potent inducer of neovascularization, is the only angiogenic molecule known to exhibit ribonucleolytic activity. Its overall structure, as determined at 2.4 A, is similar to that of pancreatic ribonuclease A, but it differs markedly in several distinct areas, particularly the ribonucleolytic active center and the putative receptor binding site, both of which are critically involved in biological function. Most strikingly, the site that is spatially analogous to that for pyrimidine binding in ribonuclease A differs significantly in conformation and is "obstructed" by glutamine-117. Movement of this and adjacent residues may be required for substrate binding to angiogenin and, hence, constitute a key part of its mechanism of action.

A statistical analysis of side-chain conformations in proteins: comparison with ECEPP predictions

A comparison of the statistical distributions of side-chain conformations of 17 amino acids (Gly, Ala, and Pro excluded), observed in 63 nonhomologous globular proteins (covering 10,832 residues), is made with similar distributions calculated from the low-energy conformational states for the same amino acids (blocked with acetyl and N-methylamide groups at the N- and C-termini, respectively) obtained by Vásquez et al. [(1983), Macromolecules 16, 1043-1049] using the ECEPP/2 force field. Those residues (i) with linear side chains (Arg, Lys, Met, Cys, Ser), or those that are unbranched through the gamma-carbon atom (Glu, Gln) show good agreement, whereas (ii) those with side chains that are branched at C beta or C gamma show poor agreement with ECEPP calculations. A possible explanation for this is shown to be the greater tendency for side-chain atoms in class (ii) to interact with the backbone and/or adjacent side chains. Accordingly, ECEPP/3 calculations, carried out after elongating the backbone chain of the model peptide unit (by adding three Ala residues on each side of the central residue, and then blocking the termini as before), result in distributions that are often closer to the observed side-chain distributions. The implications of these results for the relative importance of short-range versus long-range interactions in determining protein structure are discussed.

Alteration of the enzymatic specificity of human angiogenin by site-directed mutagenesis

The molecular basis for the enzymatic specificity of human angiogenin has been investigated by site-directed mutagenesis of Thr-44, Glu-108, and Ser-118--residues corresponding to those thought to be involved in substrate base recognition in the homologous protein, RNase A. Mutations of Thr-44 to Ala, His, and Asp affect both activity and specificity dramatically. The Ala and His replacements decrease activity toward tRNA by factors of 25 and 40, respectively, and reduce cleavage of cytidylyl more than uridylyl dinucleotides. Substitution by Asp does not influence the rate of tRNA and rRNA degradation but alters specificity even more markedly than the other mutations: T44D-angiogenin has 17-40-fold decreased activity toward CpN' dinucleotides and 1.3-1.9-fold increased activity toward UpN', resulting in an inverted order of preference (U > C) compared to native angiogenin. Mutations of Glu-108 to Lys and Gln change activity toward RNA and dinucleotides by no more than 50% and produce slight increases in preference for adenosine vs guanosine at position N' of NpN' substrates. Mutations of Ser-118 to Asp and Arg have a larger effect, decreasing activity by factors of approximately 2 and 4, respectively, toward all substrates examined. These results indicate that: (i) Thr-44 is important for recognition of the pyrimidine moiety at position N, (ii) Glu-108 may make a small contribution to binding the N'-nucleotide, and (iii) Ser-118 has a minor functional role, which appears to involve catalysis rather than nucleotide binding.(ABSTRACT TRUNCATED AT 250 WORDS)

A novel parameterization scheme for energy equations and its use to calculate the structure of protein molecules

A novel scheme for the parameterization of a type of "potential energy" function for protein molecules is introduced. The function is parameterized based on the known conformations of previously determined protein structures and their sequence similarity to a molecule whose conformation is to be calculated. Once parameterized, minima of the potential energy function can be located using a version of simulated annealing which has been previously shown to locate global and near-global minima with the given functional form. As a test problem, the potential was parameterized based on the known structures of the rubredoxins from Desulfovibrio vulgaris, Desulfovibrio desulfuricans, and Clostridium pasteurianum, which vary from 45 to 54 amino acids in length, and the sequence alignments of these molecules with the rubredoxin sequence from Desulfovibrio gigas. Since the Desulfovibrio gigas rubredeoxin conformation has also been determined, it is possible to check the accuracy of the results. Ten simulated-annealing runs from random starting conformations were performed. Seven of the 10 resultant conformations have an all-C alpha rms deviation from the crystallographically determined conformation of less than 1.7 A. For five of the structures, the rms deviation is less than 0.8 A. Four of the structures have conformations which are virtually identical to each other except for the position of the carboxy-terminal residue. This is also the conformation which is achieved if the determined crystal structure is minimized with the same potential. The all-C alpha rms difference between the crystal and minimized crystal structures is 0.6 A.(ABSTRACT TRUNCATED AT 250 WORDS)

Dual site model for the organogenic activity of angiogenin

The residues that are indispensable for the ribonucleolytic activity of angiogenin are also known to be essential for its angiogenic activity. We now demonstrate that residues in another region of the protein, devoid of catalytic residues, are additionally required for angiogenesis. Endoproteinase Lys-C or a baby hamster kidney cell protease cleaves angiogenin at the peptide bond either between Lys-60 and Asn-61 or between Glu-67 and Asn-68, respectively. The two polypeptide fragments resulting from either cleavage remain linked by disulfide bonds. These two derivatives and des-(Asn61-Glu67)-angiogenin--in which both bonds are cleaved--retain their ribonucleolytic activities toward tRNA, 18S and 28S rRNA, and dinucleoside phosphates but are no longer angiogenic on the chicken embryo chorioallantoic membrane. Further, their capacity to elicit a second messenger response in endothelial cells is greatly decreased. Moreover, none of these three derivatives inhibit angiogenin-induced angiogenesis. This contrasts with two active site mutants of angiogenin. These results identify the residues from 60 to 68 as a region of angiogenin that is part of a cell-surface receptor binding site [see accompanying manuscript: Hu, G.-F., Chang, S.-I., Riordan, J.F. & Vallee, B.L. (1991) Proc. Natl. Acad. Sci. USA 88, 2227-2231] and serve as the basis for a dual site model of the organogenic activity of angiogenin.

A critical evaluation of the predicted and X-ray structures of alpha-lactalbumin

The rapidly increasing availability of protein amino-acid sequences, many of which have been determined from the corresponding gene sequences, has intensified interest in the prediction of related protein structures when the three-dimensional structure of another member of the family is known. The study of bovine alpha-Lactalbumin provides a classic example in which the three-dimensional structure was predicted, first by Browne et al. (1969) and later by Warme et al. (1974), from the three-dimensional structure of hen-egg-white lysozyme (Blake et al., 1965), taking into account the striking relationship between the amino acid sequences of the two proteins. A comprehensive comparison of these models with the structure of baboon alpha-Lactalbumin derived from X-ray crystallography (Acharya et al., 1989) is presented. The models mostly compare well with the experimentally determined structure except in the flexible C-terminal region of the molecule (rms deviation on C alpha s of residues 1-95, 1.1 A).

Replacement of residues 8-22 of angiogenin with 7-21 of RNase A selectively affects protein synthesis inhibition and angiogenesis

The region of human angiogenin containing residues 8-21 is highly conserved in angiogenins from four mammalian species but differs substantially from the corresponding region of the homologous protein ribonuclease A (RNase A). Regional mutagenesis has been employed to replace this segment of angiogenin with the corresponding RNase A sequence, and the activities of the resulting covalent angiogenin/RNase hybrid, designated ARH-III, have been examined. The ribonucleolytic activity of ARH-III is unchanged toward most substrates, including tRNA, naked 18S and 28S rRNA, CpA, CpG, UpA, and UpG. In contrast, the capacity of ARH-III to inhibit cell-free protein synthesis is decreased 20-30-fold compared to that of angiogenin. The angiogenic activity of ARH-III is also different; it is actually more potent. It induces a maximal response in the chick chorioallantoic membrane assay at 0.1 ng per egg, a 10-fold lower dose than required for angiogenin. In addition, binding of ARH-III to the placental ribonuclease inhibitor is increased by at least 1 order of magnitude (Ki less than or equal to 7 x 10(-17) M) compared to angiogenin. Thus, mutation of a highly conserved region of angiogenin markedly affects those properties likely involved in its biological function(s); it does not, however, alter ribonucleolytic activity toward most substrates.

Presence of a basic amino acid residue at either position 66 or 122 is a condition for enzymic activity in the ribonuclease superfamily

Some members of the ribonuclease superfamily differ at more than 50% of the amino acid positions. Although the three-dimensional structures probably are very similar and the active-site residues have been conserved, other substrate-binding regions have changed considerably. Several proteins in the superfamily are active ribonucleases while other exhibit practically no enzymic activity. The presence of a basic residue at either position 66 or 122 appears to be a condition for ribonuclease activity.

Binding of placental ribonuclease inhibitor to the active site of angiogenin

The importance of specific residues in angiogenin for binding to placental ribonuclease inhibitor (PRI) has been assessed by examining the interaction of angiogenin derivatives with PRI. PRI binds native angiogenin with a Ki value of 7.1 X 10(-16) M [Lee, F. S., Shapiro, R., & Vallee, B. L. (1989) Biochemistry 28, 225-230]. Substitution of a Gln for Lys-40 in angiogenin by site-specific mutagenesis decreases the association rate constant 3-fold and increases the dissociation rate constant 440-fold, resulting in a 1300-fold weaker Ki value. The half-life of the mutant.PRI complex is 3.4 h compared to approximately 60 days for the native angiogenin.PRI complex. The magnitude of the change in Ki value suggests that in the complex, Lys-40 forms a salt bridge or hydrogen bond with an anionic moiety in PRI. Carboxymethylation of His-13 or His-114 with bromoacetate increases the Ki value 15-fold, and oxidation of Trp-89 by means of dimethyl sulfoxide and hydrochloric acid increases it 2.4-fold, suggesting that these residues also form part of the contact region with PRI. The changes in Ki value reflect an increase in the dissociation rate constant. On the other hand, dinitrophenylation of either Lys-50 or Lys-60 with 1-fluoro-2,4-dinitrobenzene does not significantly alter the Ki value, suggesting that these residues are not part of the contact region. These results indicate that PRI inhibition minimally involves the three residues critical for the activity of angiogenin--Lys-40, His-13, and His-114--and to a lesser extent its single tryptophan, Trp-89.

A covalent angiogenin/ribonuclease hybrid with a fourth disulfide bond generated by regional mutagenesis

Human angiogenin is a blood vessel inducing protein whose primary structure displays 33% identity to that of bovine pancreatic ribonuclease A (RNase A). Angiogenin catalyzes limited cleavage of 18S and 28S ribosomal RNA and is several orders of magnitude less potent than RNase A toward conventional substrates. A striking structural difference between angiogenin and RNase is the virtual absence of sequence similarity within the region of RNase that contains the Cys-65--Cys-72 disulfide bond. Indeed, angiogenin lacks this disulfide linkage. The present report describes the use of regional mutagenesis to generate a covalent angiogenin/RNase hybrid protein, ARH-I, where residues 58-70 of angiogenin have been replaced by the corresponding segment of RNase A (residues 59-73). The protein expressed in Escherichia coli readily folds at pH 8.5 to form the four expected disulfide bonds. The in vivo angiogenic potency of ARH-I is markedly diminished compared with that of angiogenin when examined using the chick chorioallantoic membrane assay. In contrast, its enzymatic activity is dramatically increased. With high molecular weight wheat germ RNA and tRNA, ARH-I is 660- and 300-fold more active than angiogenin, respectively, while with poly(uridylic acid), poly(cytidylic acid), cytidylyl(3'----5')adenosine (CpA), and uridylyl(3'----5')adenosine (UpA) activity is enhanced by about 200-fold. In addition, the specificity of ARH-I toward dinucleoside 3',5'-phosphates is qualitatively similar to RNase A; while angiogenin prefers cytidylyl(3'----5')guanosine (CpG) to UpA, both RNase and the hybrid prefer UpA to CpG. ARH-I also displays greater than 10-fold enhanced activity toward rRNA in intact ribosomes, while abolishing the capacity of the ribosome to support cell-free protein synthesis. The enhanced enzymatic properties of ARH-I parallel a 2-fold increase in chemical reactivity of active-site lysine and histidine residues based on rates of chemical modification. The data indicate that introduction of a region of RNase A containing the Cys-65--Cys-72 disulfide bond into angiogenin dramatically increases RNase-like enzymatic activity while reducing its angiogenicity.

Role of lysines in human angiogenin: chemical modification and site-directed mutagenesis

The role of lysines in the ribonucleolytic and angiogenic activities of human angiogenin has been examined by chemical modification and site-directed mutagenesis. It was demonstrated previously [Shapiro, R., Weremowicz, S., Riordan, J.F., & Vallee, B.L. (1987) Proc. Natl. Acad. Sci. U.S.A. 84, 8783-8787] that extensive treatment with lysine reagents markedly decreases the ribonucleolytic activity of angiogenin. In the present study, limited chemical modification with 1-fluoro-2,4-dinitrobenzene followed by C18 high-performance liquid chromatography yielded several (dinitrophenyl)angiogenin derivaties. The major derivative formed had slightly increased enzymatic activity compared with the unmodified protein. Tryptic peptide mapping demonstrated the site of modification to be Lys-50. A second derivative, modified at Lys-60, was 34% active. Analysis of a third derivative indicated that modification of Lys-82 did not decrease activity. Thus, Lys-50 and Lys-82 are unessential for enzymatic activity while Lys-60 may play a minor role. No pure derivative modified at Lys-40, corresponding to the active-site residue Lys-41 of the homologous protein ribonuclease A, could be obtained by chemical procedures. Therefore, we employed oligonucleotide-directed mutagenesis to replace this lysine with glutamine or arginine. The Gln-40 derivative had less than 0.05% enzymatic activity compared with the unmodified protein and substantially reduced angiogenic activity when examined with the chick embryo chorioallantoic membrane assay. These results suggest that the angiogenic activity of the protein is dependent on an intact enzymatic active site. The Arg-40 derivative had 2.2% ribonucleolytic activity compared with unmodified angiogenin. The effects of reductive methylation of this derivative indicate that no lysines other than Lys-40 are critical.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular modeling of calmodulin: a comparison with crystallographic data

Two methods of side-chain placement on a modeled protein have been examined. Two molecular models of calmodulin were constructed that differ in the treatment of side chains prior to optimization of the molecule. A virtual bond analysis program developed by Purisima and Scheraga was used to determine the backbone conformation based on 2.2 angstroms resolution C alpha coordinates for the molecules. In the first model, side chains were initially constructed in an extended conformation. In the second model, a conformational grid search technique was employed. Calcium ions were treated explicitly during energy optimization using CHARMM. The models are compared to a recently published refined crystal structure of calmodulin. The results indicate that the initial choices for side-chains, but also significant effects on the main-chain conformation and supersecondary structure. The conformational differences are discussed. Analysis of these and other methods makes possible the formulation of a methodology for more appropriate side-chain placement in modeled proteins.

Conformational characterization of human angiogenin by limited proteolysis

The primary structure of angiogenin is 33% identical to that of bovine pancreatic ribonuclease (RNase), but the enzymatic activities of the two proteins differ markedly. Similarly, their susceptibilities to limited proteolysis differ as well. In contrast to RNase, angiogenin totally resists proteolysis by subtilisin. Indeed, among 16 proteases examined, only endoprotease Lys-C, trypsin, and pepsin are able to cleave angiogenin. Even with prolonged incubation, endoprotease Lys-C selectively cleaves the Lys-60-Asn-61 bond; the product retains full ribonucleolytic activity. Initially, trypsin also cleaves this same bond, but with time it causes extensive degradation. Pepsin, at pH 2, cleaves the Phe-9-Leu-10 bond, to give angiogenin (10-123), which displays approximately 15% of the native activity toward ribosomal RNA (rRNA). The susceptibility to proteolysis and/or the sites of cleavage of angiogenin and bovine RNase differ markedly despite their structural homology. These differences are considered in terms of the amino acid sequences of the two proteins.

Human angiogenin, an organogenic protein

Angiogenin is a 14 kD protein, initially isolated as a tumour-cell secreted product but subsequently found to be a normal constituent of human plasma. It is a potent inducer of blood vessel formation on the chorioallantoic membrane of the chick embryo. Chemical characterization of the protein reveals a remarkable homology to the pancreatic ribonuclease family and has led to the identification of a unique ribonucleolytic activity for angiogenin. It is a particularly potent inhibitor of in vitro protein synthesis. Treatment with placental ribonuclease inhibitor abolishes the biological and enzymatic activities of angiogenin, an effect with important mechanistic, physiological and pharmacologic implications.

Computers in molecular biology: current applications and emerging trends

The rate of generation of molecular sequence data is forcing the use of computers as a central tool in molecular biology. Current use of computers is limited largely to data management and sequence comparisons, but rapid growth in the volume of data is generating pressure for the development of high-speed analytical methods for deciphering the codes connecting nucleotide sequence with protein structure and function.

Calculation of protein conformation by the build-up procedure. Application to bovine pancreatic trypsin inhibitor using limited simulated nuclear magnetic resonance data

Low-energy conformations of a set of tetrapeptides derived from the small protein bovine pancreatic trypsin inhibitor (BPTI) were generated by a build-up procedure from the low-energy conformations of single amino acid residues. At each stage, various-size fragments were built up from all combinations of smaller ones, the total energies were then minimized, and the low-energy conformations were retained for the next stage. The energies of the tetrapeptides were re-ordered by including the effects of hydration. No information other than the amino acid sequence was used to obtain the low-energy conformations of the hydrated tetrapeptides. The latter were then supplemented with a limited set of simulated NMR distance information, derived from the X-ray structure of BPTI, to provide a basis for building the rest of the whole protein molecule by the same procedure. A total of 189 upper bounds, plus 12 pairs of upper and lower bounds pertaining to the location of the three disulfide bonds in this molecule, were used. Four sets of conformations of the entire molecule were generated by utilizing different combinations of smaller fragments. It was possible to obtain low-energy conformations with small rms deviations, 1.1 to 1.4 A for the alpha-carbons, from the structure derived by X-ray diffraction. The average deviations of the backbone dihedral angles were also low, viz. 23 degrees to 26 degrees.

Interpreting the behavior of enzymes: purpose or pedigree?

To interpret the growing body of data describing the structural, physical, and chemical behaviors of biological macromolecules, some understanding must be developed to relate these behaviors to the evolutionary processes that created them. Behaviors that are the products of natural selection reflect biological function and offer clues to the underlying chemical principles. Nonselected behaviors reflect historical accident and random drift. This review considers experimental data relevant to distinguishing between nonfunctional and functional behaviors in biological macromolecules. In the first segment, tools are developed for building functional and historical models to explain macromolecular behavior. These tools are then used with recent experimental data to develop a general outline of the relationship between structure, behavior, and natural selection in proteins and nucleic acids. In segments published elsewhere, specific functional and historical models for three properties of enzymes--kinetics, stereospecificity, and specificity for cofactor structures--are examined. Functional models appear most suitable for explaining the kinetic behavior of proteins. A mixture of functional and historical models appears necessary to understand the stereospecificity of enzyme reactions. Specificity for cofactor structures appears best understood in light of purely historical models based on a hypothesis of an early form of life exclusively using RNA catalysis.

Ribonucleolytic activity of angiogenin: essential histidine, lysine, and arginine residues

The homology of angiogenin and pancreatic RNase A provides a compelling reason to systematically compare the characteristics of the two proteins using the chemical modification approaches that proved essential to understanding the action of RNase. Reagents specific for histidine, lysine, and arginine markedly decrease the ribonucleolytic activity of angiogenin, much as has been observed for RNase A. Activity is abolished by reduction of the disulfide bonds and is restored by reoxidation. Methionine, tyrosine, and carboxyl group reagents have no significant effect. From the point of view of reactivity, the histidine and lysine residues in angiogenin are severalfold less susceptible to modification than those in RNase A. Arginine reagents, on the other hand, inactivate angiogenin considerably faster than RNase A. Considering specificity, bromoacetate inactivates angiogenin at pH 5.5 by modifying 1.5 histidines, but lysine and arginine reagents are less specific. Thus, 3.8 and 6.3 residues, respectively, are modified by 1-fluoro-2,4-dinitrobenzene and by formaldehyde plus cyanoborohydride, under conditions where activity decreases by approximately 80% in both cases. With phenylglyoxal, 6.7 arginines are lost when there is 92% inactivation. Poly(G) prevents inactivation by lysine and arginine reagents, and phosphate protects against the effects of lysine modification. Thus, the functional consequences of these modifications likely reflect the loss of critical residues rather than general conformational effects.

Human placental ribonuclease inhibitor abolishes both angiogenic and ribonucleolytic activities of angiogenin

Human placental ribonuclease inhibitor (PRI) abolishes both the ribonucleolytic activity of angiogenin toward 28S and 18S rRNA and its angiogenic activity on the chicken embryo chorioallantoic membrane. Treatment of the angiogenin-PRI complex with p-hydroxymercuribenzoate releases enzymatically active angiogenin. Assays measuring competition between angiogenin and bovine pancreatic ribonuclease A for PRI reveal that binding of the inhibitor to angiogenin is extremely tight, with a Ki value well below 0.1 nM. The stability of the angiogenin-PRI complex was assessed by cation-exchange HPLC quantitation of free angiogenin. No significant dissociation was detected after 17 hr at 25 degrees C in the presence of a large excess of bovine ribonuclease, which serves as a scavenger for free inhibitor. The results of these experiments, based on the predictive capacity of the angiogenin/RNase homology, suggest that PRI and related inhibitors may participate in the in vivo regulation of angiogenin and that this might have pharmacologic and/or therapeutic implications.

Knowledge-based prediction of protein structures and the design of novel molecules

Prediction of the tertiary structures of proteins may be carried out using a knowledge-based approach. This depends on identification of analogies in secondary structures, motifs, domains or ligand interactions between a protein to be modelled and those of known three-dimensional structures. Such techniques are of value in prediction of receptor structures to aid the design of drugs, herbicides or pesticides, antigens in vaccine design, and novel molecules in protein engineering.

Calculating three-dimensional changes in protein structure due to amino-acid substitutions: the variable region of immunoglobulins

A procedure (coupled perturbation procedure, CPP) is introduced as a specific method for calculating the detailed three-dimensional structure of a protein molecule which has a number of amino-acid substitutions relative to some previously determined "parent" protein structure. The accuracy of the procedure is tested by calculating the conformation of a region of the human immunoglobulin fragment Fab Kol based on the analogous region of the human immunoglobulin fragment Fab New. Both structures have previously been determined crystallographically. The calculated model is accurate to the extent that both of the sequence differences in the region are modeled correctly and that conformational changes in a number of nearby residues are correctly identified. CPP is shown to give better results than other commonly used modeling procedures when applied to the same problem.