Structural analysis of carboxypeptidase A and its complexes with inhibitors as a basis for modeling enzyme recognition and specificity

A Graphic Encoding Method for Quantitative Classification of Protein Structure and Representation of Conformational Changes

In order to successfully predict a proteins function throughout its trajectory, in addition to uncovering changes in its conformational state, it is necessary to employ techniques that maintain its 3D information while performing at scale. We extend a protein representation that encodes secondary and tertiary structure into fix-sized, color images, and a neural network architecture (called GEM-net) that leverages our encoded representation. We show the applicability of our method in two ways: (1) performing protein function prediction, hitting accuracy between 78 and 83 percent, and (2) visualizing and detecting conformational changes in protein trajectories during molecular dynamics simulations.

Searching techniques for databases of protein secondary structures

This paper summarizes the findings of a recent, British Library-funded research project into computer techniques for searching the three-dimensional protein structures that occur in the Protein Data Bank. The work focuses on the secondary structures of proteins and utilizes both angular and distance geometric information. Algorithms are presented for the auto matic identification of secondary structure elements, of sec ondary structure motifs and of proteins with similar secondary structures.

Progress in metallocarboxypeptidases and their small molecular weight inhibitors

In what corresponds to a life span, metallocarboxypeptidases (MCPs) have jumped from being mere contaminants in animal pancreas powders (in depression year 1929) to be key players in cellular and molecular processes (in yet-another-depression years 2009-2010). MCPs are unique zinc-dependent enzymes that catalyze the breakdown of the amide bond at the C-terminus of peptide and protein substrates and participate in the recovery of dietary amino acids, tissue organogenesis, neurohormone and cytokine maturation and other important physiological processes. More than 26 genes code for MCPs in the human genome, many of them still waiting to be fully understood in terms of physiological function. A variety of MCPs have been linked to diseases in man: acute pancreatitis and pancreas cancer, type 2 diabetes, Alzheimer's Disease, various types of cancer, and fibrinolysis and inflammation. Many of these discoveries have been made possible thanks to recent advances, as exemplified by plasma carboxypeptidases N and B, known for fifty and twenty years, respectively, which have had their structures released only very recently. Plasma carboxypeptidase B is a biological target for therapy because of its involvement in the coagulation/fibrinolysis processes. Besides, the widespread use of carboxypeptidase A as a benchmark metalloprotease since the early days of Biochemistry has allowed the identification and design of an increasingly vast repertory of small molecular weight inhibitors. With these two examples we wish to emphasize that MCPs have become part of the drug discovery portfolio of pharmaceutical companies and academic research laboratories. This paper will review key developments in the discovery and design of MCP small molecular weight inhibitors, with an emphasis on the discovery of chemically diverse entities. Although encouraging advances have been achieved in the last few years, the specificity and oral bioavailability of the new chemotherapeutic agents seem to pose a challenge to medicinal chemists.

Analysis of a new crystal form of procarboxypeptidase B: further insights into the catalytic mechanism

A new triclinic crystal structure form of porcine pancreatic procarboxypeptidase B (PCPB) was obtained at higher resolution than the previously known tetragonal crystal structure. This new crystal polymorph has allowed for a corrected, accurate assignment of residues along the polypeptide chain based on the currently available gene sequence information and crystallographic data. The present structure shows unbound PCPB in a distinct molecular packing as compared to the previous benzamidine complexed form. Its catalytically important Tyr248 residue is oriented and hydrogen-bonded to solvent water molecules, and locates the furthest away from the catalytic zinc ion as compared to previous structures. A relatively long stretch of residues flanking Tyr248 and guarding the access to the catalytic zinc ion was found to be sequentially unique to the M14 family of peptidases. Predictions from a normal mode analysis indicated that this stretch of residues belongs to a rigid subdomain in the protein structure. The specific presence of a tyrosyl residue at the most exposed position in this region would allow for a delicate balance between extreme hydrophobicity and hydrophilicity, and affect substrate binding and the kinetic efficiency of the enzyme.

Rapid detection of similarity in protein structure and function through contact metric distances

The characterization of biological function among newly determined protein structures is a central challenge in structural genomics. One class of computational solutions to this problem is based on the similarity of protein structure. Here, we implement a simple yet efficient measure of protein structure similarity, the contact metric. Even though its computation avoids structural alignments and is therefore nearly instantaneous, we find that small values correlate with geometrical root mean square deviations obtained from structural alignments. To test whether the contact metric detects functional similarity, as defined by Gene Ontology (GO) terms, it was compared in large-scale computational experiments to four other measures of structural similarity, including alignment algorithms as well as alignment independent approaches. The contact metric was the fastest method and its sensitivity, at any given specificity level, was a close second only to Fast Alignment and Search Tool—a structural alignment method that is slower by three orders of magnitude. Critically, nearly 40% of correct functional inferences by the contact metric were not identified by any other approach, which shows that the contact metric is complementary and computationally efficient in detecting functional relationships between proteins. A public ‘Contact Metric Internet Server’ is provided.

Structural preference for changes in the direction of the Ca2+-induced transition: a study of the regulatory domain of skeletal troponin-C

The determinants for specificity in the Ca(2+)-dependent response of the regulatory N-terminal domain of skeletal troponin-C are a combination of intrinsic and induced properties. We characterized computationally the intrinsic propensity of this domain for structural changes similar to those observed experimentally in the Ca(2+)-induced transition. The preference for such changes was assessed by comparing the structural effect of the harmonic and quasiharmonic vibrations specific for each Ca(2+) occupancy with crystallographic data. Results show that only the Ca(2+)-saturated form of the protein features a slow vibrational motion preparatory for the transition. From the characteristics of this mode, we identified a molecular mechanism for transition, by which residues 42-51 of helix B and of the adjacent linker move toward helices (A, D), and bind to the surface used by the protein to interact with troponin-I. By obstructing the access of the target to hydrophobic residues important in the formation of the complex, helix B and the adjacent linker act as an autoinhibitory structural element. Specific properties of the methionines at the interaction surface were found to favor the binding of the autoinhibitory region. Located over hydrophobic residues critical for binding, the methionines are easily displaceable to increase the accessibility of these residues to molecular encounter.

Protein structural alignments and functional genomics

Structural genomics-the systematic solution of structures of the proteins of an organism-will increasingly often produce molecules of unknown function with no close relative of known function. Prediction of protein function from structure has thereby become a challenging problem of computational molecular biology. The strong conservation of active site conformations in homologous proteins suggests a method for identifying them. This depends on the relationship between size and goodness-of-fit of aligned substructures in homologous proteins. For all pairs of proteins studied, the root-mean-square deviation (RMSD) as a function of the number of residues aligned varies exponentially for large common substructures and linearly for small common substructures. The exponent of the dependence at large common substructures is well correlated with the RMSD of the core as originally calculated by Chothia and Lesk (EMBO J 1986;5:823-826), affording the possibility of reconciling different structural alignment procedures. In the region of small common substructures, reduced aligned subsets define active sites and can be used to suggest the locations of active sites in homologous proteins.

Extent and nature of contacts between protein molecules in crystal lattices and between subunits of protein oligomers

A survey was compiled of several characteristics of the intersubunit contacts in 58 oligomeric proteins, and of the intermolecular contracts in the lattice for 223 protein crystal structures. The total number of atoms in contact and the secondary structure elements involved are similar in the two types of interfaces. Crystal contact patches are frequently smaller than patches involved in oligomer interfaces. Crystal contacts result from more numerous interactions by polar residues, compared with a tendency toward nonpolar amino acids at oligomer interfaces. Arginine is the only amino acid prominent in both types of interfaces. Potentials of mean force for residue-residue contacts at both crystal and oligomer interfaces were derived from comparison of the number of observed residue-residue interactions with the number expected by mass action. They show that hydrophobic interactions at oligomer interfaces favor aromatic amino acids and methionine over aliphatic amino acids; and that crystal contacts form in such a way as to avoid inclusion of hydrophobic interactions. They also suggest that complex salt bridges with certain amino acid compositions might be important in oligomer formation. For a protein that is recalcitrant to crystallization, substitution of lysine residues with arginine or glutamine is a recommended strategy.

Systematic representation of protein folding patterns

A tabular representation of protein folding patterns is described, which comprises information about the order along the chain of helices and strands of sheet, identifies the elements of secondary structure that interact, and indicates their relative orientation. These tableaux are intelligible to both people and computers, and support the application of algorithms for identification of proteins with similar folding patterns. Their inclusion in a database of protein structures would support investigations of structural relationships at the topological level.

Three-dimensional searching for recurrent structural motifs in data bases of protein structures

The problem of searching a data base of coordinates of proteins for substructures similar to a probe structure or motif is an important problem in computational molecular biology. It is the three-dimensional analog of the one-dimensional case of pattern matching in strings, procedures for which are widely used in molecular biology to search data bases of gene sequences. Typical applications of substructure searching are: (i) Determining whether structural features observed in one protein structure are unique or recurrent, and (ii) in predictions of protein structures, to bridge gaps in an incomplete structural model, by searching the data base for peptides that link the given starting and ending points. We describe our analysis of the problem and our experience in developing software.

Generation of a substructure library for the description and classification of protein secondary structure. I. Overview of the methods and results

Protein secondary structure has been typically classified into four major classes--alpha-helices, extended strands, reverse turns, and loops. Available methods for secondary structure analysis utilize predefined structure templates to search for structural matches among proteins. By this approach a significant portion of a proteins backbone conformation is assigned to one of a limited number of conformations or, if unassigned, to random coil. To expand our ability to describe protein secondary structure, we have developed an algorithm that operates independently of a predefined structure template. The procedure uses two geometric descriptors, the linear distance and the backbone dihedral angle, to represent the conformation form the alpha-carbon coordinates. The algorithm functions by searching for conformationally equivalent, contiguous fragments without regard to secondary structural classification and is thus independent of the complexity of the backbone fold. The result is a library of conformationally equivalent structure fragments that exhibit some novel characteristics. The library contains features that reproduce the major secondary structure classes as well as defining conformations previously described only as random or undefined conformations. Additionally, the library defines several subclassifications of beta-strands. We present here a validation of this method and a presentation and discussion of the most significant results. In a second study, we report the results of application of this method to spectra-structure correlations in Fourier transform infrared spectroscopy.

Conformation and fluctuations of free stefin B: a molecular dynamics study

Molecular dynamics study was performed on the cysteine proteinase inhibitor stefin B. Structure of inhibitor from the complex with papain was used as a starting point. Amino terminal "trunk" of the inhibitor which lies extended along the cleft of the enzyme in the complex, folded onto the body of inhibitor during MD simulation, thereby reducing the total and particularly hydrophobic surface exposed to the solvent. This effect counterbalances hydrophobic contribution of the "trunk" and explains why its deletion in stefin B and related inhibitors doesn't reduce the dissociation constant. The rest of stefin B conformation is conserved together with main chain hydrogen bonds. Fluctuations of C alpha atoms resembles crystallographic B factors with exception of residues in contact with enzyme.

Implementing knot-theoretical characterization methods to analyze the backbone structure of proteins: application to CTF L7/L12 and carboxypeptidase A inhibitor proteins

In this work we apply a recently developed method for characterizing the shape of the tertiary structure of proteins. The approach is based on a combination of graph- and knot-theoretical characterizations of Cartesian projections of the space curve describing the protein backbone. The proposed technique reduces the essential shape features to a topologically based code formed by a sequence of knot symbols and polynomials. These polynomials are topological invariants that describe the overcrossing and knotting patterns of curves derived from the molecular space curve. These descriptors are algorithmically computed. The procedure is applied to describe the structure of the carboxy terminal fragment of the L7/L12 chloroplast ribosomal protein (CTF L7/L12) and the potato carboxypeptidase A inhibitor protein (PCI), which has a set of three disulfide bridges. In the former case, we describe the protein's shape features in terms of its alpha-helices, and a backbone simplified by considering helices without internal structure. An extension of the methodology to describe disulfide bridges is discussed and applied to PCI. Changes in the knot-theoretical characterization due to possible uncertainties in the resolution of the X-ray structure, as well as the inclusion of low-frequency motions of the backbone, are also discussed.

A fast unbiased comparison of protein structures by means of the Needleman-Wunsch algorithm

A fast dynamic programming algorithm for the spatial superposition of protein structure without prior knowledge of an initial alignment has been developed. The program was applied to serine proteases, hemoglobins, cytochromes C, small copper-binding proteins, and lysozymes. In most cases the existing structural homology could be detected in a completely unbiased way. The results of the method presented are in general agreement with other studies. Applying our method, the different alignment results obtained by other authors for serine proteases and cytochromes C can be classified in terms of different alignment parameters such as gap penalties or cut-off length. Limitations of the method are discussed.

Use of techniques derived from graph theory to compare secondary structure motifs in proteins

A substructure matching algorithm is described that can be used for the automatic identification of secondary structural motifs in three-dimensional protein structures from the Protein Data Bank. The proteins and motifs are stored for searching as labelled graphs, with the nodes of a graph corresponding to linear representations of helices and strands and the edges to the inter-line angles and distances. A modification of Ullman's subgraph isomorphism algorithm is described that can be used to search these graph representations. Tests with patterns from the protein structure literature demonstrate both the efficiency and the effectiveness of the search procedure, which has been implemented in FORTRAN 77 on a MicroVAX-II system, coupled to the molecular fitting program FRODO on an Evans and Sutherland PS300 graphics system.

Dynamical structure of carboxypeptidase A

Structural fluctuations of the apoenzyme form of carboxypeptidase A (EC 3.4.12.2) have been evaluated on the basis of molecular dynamics. The Konnert-Hendrickson refined coordinates of 2437 non-hydrogen atoms of the 307 amino acid residues derived from the X-ray structure of the holoenzyme served as the molecular model together with 548 calculated polar hydrogen atoms and 25 buried solvent molecules. Molecular dynamics simulations were carried out at 277 K, and the averaged structural properties of the protein were evaluated for the terminal 20 picosecond portion of a 48 picosecond trajectory. The average atomic displacement from the initial X-ray structure was 2.49 A for all atoms and 1.79 A for C alpha atoms. The average root-mean-square (r.m.s.) fluctuation of all atoms was 0.67 A as compared to 0.54 A evaluated from the X-ray-defined temperature factors. Corresponding r.m.s. fluctuations for backbone atoms were 0.56 A by molecular dynamics and 0.49 A by X-ray. On the basis of these molecular dynamics studies of the isolated molecule, it is shown that amino acid residues corresponding to intermolecular contact sites of the crystalline enzyme are associated with high amplitude motion. All eight segments of alpha-helix and eight regions of beta-strand were well preserved except for unwinding of the five C-terminal residues of the alpha-helix 112-122 that form part of an intermolecular contact in the crystal. Four regions of beta-strand and one alpha-helix with residues adjacent to or in the active site constitute a core of constant secondary structure and are shown not to change in relative orientation to each other during the course of the trajectory. The absence of the zinc ion does not markedly influence the stereochemical relationships of active site residues in the dynamically averaged protein. The extent of motional fluctuations of each of the subsites of substrate recognition in the active site has been evaluated. Active site residues responsible for specificity of substrate binding or splitting of the scissile bond exhibit low simulated motion. In contrast, residues in more distal sites of substrate recognition exhibit markedly greater motional fluctuations. This differential extent of dynamical motion is related to structural requirements of substrate hydrolysis.

Comparing short protein substructures by a method based on backbone torsion angles

An efficient algorithm was characterized that determines the similarity in main chain conformation between short protein substructures. The algorithm computes delta t, the root mean square difference in phi and psi torsion angles over a small number of amino acids (typically 3-5). Using this algorithm, large numbers of protein substructure comparisons were feasible. The parameter delta t was sensitive to variations in local protein conformation, and it correlates with delta r, the root mean square deviation in atomic coordinates. Values for delta t were obtained that define similarity thresholds, which determine whether two substructures are considered structurally similar. To set a lower bound on the similarity threshold, we estimated the component of delta t due to measurement noise from comparisons of independently refined coordinates of the same protein. A sample distribution of delta t from nonhomologous protein comparisons identified an upper bound on the similarity threshold, one that refrains from incorporating large numbers of nonmatching comparisons. Unlike methods based on C alpha atoms alone, delta t was sensitive to rotations in the peptide plane, shown to occur in several proteins. Comparisons of homologous proteins by delta t showed that the active site torsion angles are highly conserved. The delta t method was applied to the alpha-chain of human hemoglobin, where it readily demonstrated the local differences in the structures of different ligation states.

PKB: a program system and data base for analysis of protein structure

PKB is a computer program system that combines a data base of three-dimensional protein structures with a series of algorithms for pattern recognition, data analysis, and graphics. By typing relatively simple commands the user may search the data base for instances of a structural motif and analyze in detail the set of individual structures that are found. The application of PKB to the study of protein folding is illustrated in three examples. The first analysis compares the conformations observed for a short sequential motif, sequences similar to the cell-attachment signal Arg-Gly-Asp. The second compares sequences observed for a conformational motif, a 16-residue beta alpha beta unit. The third analysis considers a population of substructures containing ion-pair interactions, examining the relationship of frequency of occurrence to calculated electrostatic energy.

Analysis of the thermal unfolding of porcine procarboxypeptidase A and its functional pieces by differential scanning calorimetry

Porcine pancreatic procarboxypeptidase A and its tryptic peptides, carboxypeptidase A and the activation segment, have been studied by high-sensitivity differential scanning calorimetry (DSC). The thermal denaturation of the zymogen and the active enzyme has been carried out at two pH values, 7.5 and 9.0, at different ionic strengths and at different scan rates. The endothermic transitions for these two proteins were always irreversible under all conditions investigated. The denaturation behaviour of both proteins seems to fit very well with the kinetic model for the DSC study of irreversible unfolding of proteins recently proposed by one of our groups. From this model, the activation energies obtained for the denaturation of the pro- and carboxypeptidase were 300 +/- 20 kJ mol-1 and 250 +/- 14 kJ mol-1 respectively. On the other hand, the isolated activation segment appears as a thermostable piece with a highly reversible thermal unfolding which follows a two-state process. The denaturation temperature observed for the isolated segment was always at least 15 K higher than those of the zymogen and the active enzyme.

Entropic elastic processes in protein mechanisms. II. Simple (passive) and coupled (active) development of elastic forces

The first part of this review on entropic elastic processes in protein mechanisms (Urry, 1988) demonstrated with the polypentapeptide of elastin (Val1-Pro2-Gly3-Val4-Gly5)n that elastic structure develops as the result of an inverse temperature transition and that entropic elasticity is due to internal chain dynamics in a regular nonrandom structure. This demonstration is contrary to the pervasive perspective of entropic protein elasticity of the past three decades wherein a network of random chains has been considered the necessary structural consequence of the occurrence of dominantly entropic elastomeric force. That this is not the case provides a new opportunity for understanding the occurrence and role of entropic elastic processes in protein mechanisms. Entropic elastic processes are considered in two classes: passive and active. The development of elastomeric force on deformation is class I (passive) and the development of elastomeric force as the result of a chemical process shifting the temperature of a transition is class II (active). Examples of class I are elastin, the elastic filament of muscle, elastic force changes in enzyme catalysis resulting from binding processes and resulting in the straining of a scissile bond, and in the turning on and off of channels due to changes in transmembrane potential. Demonstration of the consequences of elastomeric force developing as the result of an inverse temperature transition are seen in elastin, where elastic recoil is lost on oxidation, i.e., on decreasing the hydrophobicity of the chain and shifting the temperature for the development of elastomeric force to temperatures greater than physiological. This is relevant in general to loss of elasticity on aging and more specifically to the development of pulmonary emphysema. Since random chain networks are not the products of inverse temperature transitions and the temperature at which an inverse temperature transition occurs depends on the hydrophobicity of the polypeptide chain, it now becomes possible to consider chemical processes for turning elastomeric force on and off by reversibly changing the hydrophobicity of the polypeptide chain. This is herein called mechanochemical coupling of the first kind; this is the chemical modulation of the temperature for the transition from a less-ordered less elastic state to a more-ordered more elastic state. In the usual considerations to date, development of elastomeric force is the result of a standard transition from a more-ordered less elastic state to a less-ordered more elastic state.(ABSTRACT TRUNCATED AT 400 WORDS)

Molecular modeling of protein structure and function: a bioinformatic approach

This paper reports on the data/information structure of macromolecules as it extends beyond the three-dimensional conformation to include functional descriptors of biochemical (in vitro) and biological (in vivo) characteristics and as it contrasts with the limitations imposed by the data reduction and data classification techniques of traditional molecular modeling. Methodologies for structure-function representation are presented which are being incorporated within a knowledge-acquisition expert system. Examples of the bioinformatic approach are presented concerning macromolecular recognition by serine proteases and the use of Fourier transform-infrared (FT-IR) spectroscopy for structural assignment and analysis by a novel structure-perturbation approach.