An analysis of the structure of triose phosphate isomerase and its comparison with lactate dehydrogenase

Exploring Protein Fold Space

The model of protein folding proposed by Ptitsyn and colleagues involves the accretion of secondary structures around a nucleus. As developed by Efimov, this model also provides a useful way to view the relationships among structures. Although somewhat eclipsed by later databases based on the pairwise comparison of structures, Efimov’s approach provides a guide for the more automatic comparison of proteins based on an encoding of their topology as a string. Being restricted to layers of secondary structures based on beta sheets, this too has limitations which are partly overcome by moving to a more generalised secondary structure lattice that can encompass both open and closed (barrel) sheets as well as helical packing of the type encoded by Murzin and Finkelstein on small polyhedra. Regular (crystalline) lattices, such as close-packed hexagonals, were found to be too limited so pseudo-latticses were investigated including those found in quasicrystals and the Bernal tetrahedron-based lattice that he used to represent liquid water. The Bernal lattice was considered best and used to generate model protein structures. These were much more numerous than those seen in Nature, posing the open question of why this might be.

Structure of glycolate oxidase from spinach

A high-resolution structure determination of glycolate oxidase from spinach is reported. X-ray data were collected on films at the synchrotron radiation source in Daresbury, England. The structure was solved by using two heavy-atom derivatives and a solvent-flattening procedure developed by B.-C. Wang. The subunit structure is essentially a structure of the eight-stranded alpha/beta-barrel type first described for triosephosphate isomerase. In addition, there are 70 residues at the NH(2) terminus and 45 residues between strand four and helix four of the barrel, which are arranged in a helical domain outside the COOH end of the parallel strands of the barrel. The active site is in a cleft between these domains with the coenzyme FMN essentially bound to the barrel and a substrate analogue, thioglycolate, bound to the helical domain. The molecule is octameric with 422 symmetry and has a 15- to 20-A-wide hole in the middle.

Evolution of feedback-inhibited beta /alpha barrel isoenzymes by gene duplication and a single mutation

The betaalpha barrel is the common protein fold of numerous enzymes and was proposed recently to be the result of gene duplication and fusion of an ancient half-barrel. The initial enzyme of shikimate biosynthesis possesses the additional feature of feedback regulation. The crystal structure and kinetic studies on chimera and mutant proteins of yeast 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthase from Saccharomyces cerevisiae inhibited by phenylalanine (Aro3p) and DAHP synthase S. cerevisiae inhibited by tyrosine (Aro4p) give insight into important regions for regulation in the enzyme: The loop, which is connecting the two half-barrels, and structural elements added to the barrel are prerequisites for regulation and form a cavity on the N-terminal side of the betaalpha barrel. In the cavity of Aro4p at position 226 is a glycine residue, which is highly conserved in all other tyrosine-regulated DAHP synthases as well. Sequence alignments with phenylalanine-regulated DAHP synthases including Aro3p show a highly conserved serine residue at this position. An exchange of glycine to serine and vice versa leads to a complete change in the regulation pattern. Therefore the evolution of these differently feedback-inhibited isoenzymes required gene duplication and a single mutation within the internal extra element. Numerous additional amino acid substitutions present in the contemporary isoenzymes are irrelevant for regulation and occurred independently.

On the evolution of alternate core packing in eightfold beta/alpha-barrels

Two sequence-related subfamilies of flavin-binding beta/alpha-barrels have been identified (the type I and type II proteins) that differ in the nature of residue packing in the core of the barrel domain. Similar observed differences in the packing of internal amino acid side chains in beta/alpha-barrels have previously been used to argue that these domains have evolved convergently toward a stable structural framework. Using structural alignments of flavin-binding barrel proteins, we demonstrate that simple genetic alterations may be responsible for switching the nature of side-chain packing observed in beta/alpha-barrels. The implication is that the 2 structural classes of beta/alpha-barrel cores can arise divergently from an ancestral barrel framework and that convergent evolution to a stable fold need not be invoked to account for the emergence of 2 classes of beta/alpha-barrel core.

alpha/beta barrel evolution and the modular assembly of enzymes: emerging trends in the flavin oxidase/dehydrogenase family

Alpha/beta barrels have an ill-defined origin. Evidence exists which favours their divergent evolution from a common ancestral barrel and convergent evolution to a stable fold. However, recent sequence and structural information for the flavin oxidase/dehydrogenase family of barrel enzymes indicate that sub-families of alpha/beta barrels have evolved divergently. The modular fusion of barrel domains with core structures from other gene families has also contributed to the evolution of related but catalytically distinct enzyme molecules within each sub-family of the flavin oxidases/dehydrogenases. An analysis of the structures and sequences of the flavin oxidases/dehydrogenases has now enabled studies focusing on the evolutionary origins and modular assembly of this important family of proteins to be initiated.

Hyperthermostable variants of a highly thermostable alpha-amylase

Genetic screening at temperatures between 70-80 degrees C far exceeds the range of growth of most bacteria, and is not applicable to isolate easily thermostable protein variants. We describe a temperature shift protocol and an in vivo screening method which allowed us to identify a hyperthermostable variant of the thermostable alpha-amylase from Bacillus licheniformis. Our strategy was to select, after hydroxylamine mutagenesis, an intragenic suppressor mutation which overcomes a mutation leading to a thermolabile enzyme. Sequence analysis of the mutated gene revealed only one change in the amino acid sequence, substituting a valine for alanine at position 209. This single amino acid replacement increased the half-life of the protein at 90 degrees C by a factor of two to three relative to the wild-type enzyme. When this substitution was combined with another stabilizing substitution (H133Y) we described previously, the stabilizing effects were additive. The half-life of the new protein was about 12 hours at 90 degrees C, corresponding to a nine to ten-fold increase over the wild-type enzyme and the industrial Bacillus licheniformis alpha-amylase Termamyl. These mutations are located in a predicted folding domain of the protein which appears crucial in determining thermal stability.

Energetic approach to the folding of alpha/beta barrels

The folding of a polypeptide into a parallel (alpha/beta)8 barrel (which is also called a circularly permuted beta 8 alpha 8 barrel) has been investigated in terms of energy minimization. According to the arrangement of hydrogen bonds between two neighboring beta-strands of the central barrel therein, such an alpha/beta barrel structure can be folded into six different types: (1) left-tilted, left-handed crossover; (2) left-tilted, right-handed crossover; (3) nontilted, left-handed crossover; (4) nontilted, right-handed crossover; (5) right-tilted, left-handed crossover; and (6) right-tilted, right-handed crossover. Here "tilt" refers to the orientational relation of the beta-strands to the axis of the central beta-barrel, and "crossover" to the beta alpha beta folding connection feature of the parallel beta-barrel. It has been found that the right-tilted, right-handed crossover alpha/beta barrel possesses much lower energy than the other five types of alpha/beta barrels, elucidating why the observed alpha/beta barrels in proteins always assume the form of right tilt and right-handed crossover connection. As observed, the beta-strands in the energy-minimized right-tilted, right-handed crossover (alpha/beta)8-barrel are of strong right-handed twist. The value of root-mean-square fits also indicates that the central barrel contained in the lowest energy (alpha/beta)8 structure thus found coincides very well with the observed 8-stranded parallel beta-barrel in triose phosphate isomerase (TIM). Furthermore, an energetic analysis has been made demonstrating why the right-tilt, right-handed crossover barrel is the most stable structure. Our calculations and analysis support the principle that it is possible to account for the main features of frequently occurring folding patterns in proteins by means of conformational energy calculations even for very complicated structures such as (alpha/beta)8 barrels.

Crystallographic analysis of ribulose 1,5-bisphosphate carboxylase from spinach at 2.4 A resolution. Subunit interactions and active site

The X-ray structure of the quaternary complex of ribulose 1,5-bisphosphate carboxylase/oxygenase from spinach with CO2, Mg2+ and a reaction-intermediate analogue (CABP) has been determined and refined at 2.4 A resolution. Cyclic non-crystallographic symmetry averaging around the molecular 4-fold axis and phase combination were used to improve the initial multiple isomorphous replacement phases. A model composed of one large subunit and one small subunit was built in the resulting electron density map, which was of excellent quality. Application of the local symmetry gave an initial model of the L8S8 molecule with a crystallographic R-value of 0.43. Refinement of this initial model was performed by a combination of conventional least-squares energy refinement and molecular dynamics simulation using the XPLOR program. Three rounds of refinement, interspersed with manual rebuilding at the graphics display, resulted in a model containing all of the 123 amino acid residues in the small subunit, and 467 of the 475 residues in the large subunit. The R-value for this model is 0.24, with relatively small deviations from ideal stereochemistry. Subunit interactions in the L8S8 molecule have been analysed and are described. The interface areas between the subunits are extensive, and bury almost half of the accessible surface areas of both the large and the small subunit. A number of conserved interaction areas that may be of functional significance have been identified and are described, and biochemical and mutagenesis data are discussed in the structural framework of the model.

Conformational and geometrical properties of idealized beta-barrels in proteins

An equation for calculating the distances between the atoms involved in forming an idealized hydrogen bond in a parallel or antiparallel beta-barrel has been derived by adjusting the corresponding data given by Pauling and Corey for a beta-sheet. Based on these distances, a geometrical optimization method was developed, by which one can generate various idealized beta-barrels: parallel or antiparallel, tilted or non-tilted, right-tilted or left-tilted. For each type of idealized beta-barrel thus obtained, the corresponding conformation and characteristic geometric parameters as well as their relationship are analyzed and discussed. Since the strand in a tilted beta-barrel traces a curve rather than a straight line on a cylinder-like surface, a regular chain in which the dihedral angles of each residue are the same cannot form a tilted beta-barrel but only a non-tilted beta-barrel. As observed, the strands of a right-tilted beta-barrel possess a very strong right-handed twist. The radii of the idealized tilted parallel and antiparallel beta-barrels are greater than those of the corresponding non-tilted ones by approximately 1 A and approximately 1.5 A, respectively. Consequently, there is relatively more room for a tilted beta-barrel to accommodate the internal side-chains, suggesting that a conformational change from a non-tilted beta-barrel to a tilted one would ease the repulsion among the crowded internal side-chains so as to make the structure more stable. The values of root-mean-square fits indicate that the idealized right-tilted beta-barrels coincide quite well with the observed beta-barrels in both parallel and antiparallel cases.

Molecular structure of flavocytochrome b2 at 2.4 A resolution

The crystal structure of flavocytochrome b2 has been solved at 3.0 A resolution by the method of multiple isomorphous replacement with anomalous scattering. Area detector data from native and two heavy-atom derivative crystals were used. The phases were refined by the B.C. Wang phase-filtering procedure utilizing the 67% (v/v) solvent content of the crystals. A molecular model was built first on a minimap and then on computer graphics from a combination of maps both averaged and not averaged about the molecular symmetry axis. The structure was extended to 2.4 A resolution using film data recorded at a synchrotron and refined by the Hendrickson-Konnert procedure. The molecule, a tetramer of Mr 230,000, is located on a crystallographic 2-fold axis and possesses local 4-fold symmetry. Each subunit is composed of two domains, one binding a heme and the other an FMN prosthetic group. In subunit 1, both the cystochrome and the flavin-binding domain are visible in the electron density map. In subunit 2 the cytochrome domain is disordered. However, in the latter, a molecule of pyruvate, the product of the enzymatic reaction, is bound at the active site. The cytochrome domain consists of residues 1 to 99 and is folded in a fashion similar to the homologous soluble fragment of cytochrome b5. The flavin binding domain contains a parallel beta 8 alpha 8 barrel structure and is composed of residues 100 to 486. The remaining 25 residues form a tail that wraps around the molecular 4-fold axis and is in contact with each remaining subunit. The FMN moiety, which is located at the C-terminal end of the central beta-barrel, is mostly sequestered from solvent; it forms hydrogen bond interactions with main- and side-chain atoms from six of the eight beta-strands. The interaction of Lys349 with atoms N-1 and O-2 of the flavin ring is probably responsible for stabilization of the anionic form of the flavin semiquinone and hydroquinone and enhancing the reactivity of atom N-5 toward sulfite. The binding of pyruvate at the active site in subunit 2 is stabilized by interaction of its carboxylate group with the side-chain atoms of Arg376 and Tyr143. Residues His373 and Tyr254 interact with the keto-oxygen atom and are involved in catalysis. In contrast, four water molecules occupy the substrate-binding site in subunit 1 and Tyr143 forms a hydrogen bond to the ordered heme propionate group. Otherwise the two flavin-binding domains are identical within experimental error.(ABSTRACT TRUNCATED AT 400 WORDS)

Energetics of the structure and chain tilting of antiparallel beta-barrels in proteins

The preferred structural pattern of antiparallel beta-barrels in proteins, described as the right-handed tilting of the peptide strands with respect to the axis of the barrel, is accounted for in terms of intra- and interchain interaction energies. It is related to the preference of beta-sheets for right-handed twisting. Conformational energy computations have been carried out on three eight-stranded antiparallel beta-barrels composed of six-residue strands, in which L-Val and Gly alternate, and having a right-handed, a left-handed, or no tilt. After energy minimization, the relative energies of these structures were 0.0, 8.6, and 46.1 kcal/mol, respectively; i.e., the right-tilted beta-barrel is favored energetically, in agreement with anti-parallel beta-barrels observed in proteins. Tilting of the barrel is favored, relative to the nontilted structure, by both intra- and interstrand interactions, because tilting allows better packing of the bulky side chains. On the other hand, the energy difference between the left- and right-tilted barrels arises essentially from intrachain interactions. This is a consequence of the preference of beta-sheets for a right-handed twist. Space limitations inside the barrel are satisfied if there is an alternation of bulky residues and residues with small or no side chain (preferably Gly) in neighboring positions on adjacent strands. Such a pattern is seen frequently in antiparallel beta-barrels of globular proteins. The computations indicate that a structure with Val...Gly pairs can be accommodated in a beta-barrel with no distortion.

Structure of the medium-chain acyl-CoA dehydrogenase from pig liver mitochondria at 3-A resolution

The three-dimensional structure of the medium-chain acyl-CoA dehydrogenase (EC 1.3.99.3) from pig liver mitochondria has been determined to 3.0-A resolution by the x-ray diffraction method. The enzyme is a tetramer of four identical 43-kDa subunits and contains one equivalent of flavin adenine dinucleotide (FAD) per subunit. The polypeptide is folded into three domains. The N-terminal and the C-terminal domains are composed mainly of alpha-helices, and the middle domain is packed with orthogonal beta-sheets. The FAD has an extended conformation: the flavin ring lies between the N-terminal and the beta-sheet domains, and the adenine moiety is found at the junction between the C-terminal and the beta-sheet domains of one subunit and the C-terminal domain of a neighboring subunit. The polypeptide chain folding near the FAD binding site is different from those observed in other flavoproteins, such as glutathione reductase and glycolate oxidase.

Structural principles of parallel beta-barrels in proteins

Eight-stranded beta-sheets in nine protein structures containing "TIM (triose phosphate isomerase) barrels" are shown to be fitted satisfactorily by hyperboloids, the generating lines of which pass through the beta-strands. Simple parameterizations of the hyperboloid model are then used to determine the constraints that govern key parameters, such as the number of strands in the barrel, and to rationalize the remarkable conservation of strand number, observed to be eight, in nearly all the known examples of parallel beta-barrels. It is shown that the requirement to exclude solvent from the barrel interior, while at the same time keeping an upper limit on strand twist and interstrand distance so as to foster extensive hydrogen bonding interactions within the sheet, imposes strong constraints on barrel geometry. A formal description of the relationships between beta-sheet twist, strand number, and barrel dimensions is given here. It could have important implications for studies of protein folding and design.

A sensitive procedure to compare amino acid sequences

Methods are discussed that provide sensitive criteria for detection of weak sequence homologies. They are based on the Dayhoff relatedness odds amino acid exchange matrix and certain residue physical characteristics. The search procedure uses several residue probe lengths in comparing all possible segments of two protein sequences, and search plots are shown with peak values displayed over the entire search length. Alignments are automatically effected using the highest search matrix values and without the necessity of gap penalties. Tests for significance are derived from actual protein sequences rather than a random shuffling procedure.

Human triose-phosphate isomerase deficiency: a single amino acid substitution results in a thermolabile enzyme

Triose-phosphate isomerase (TPI; D-glyceraldehyde-3-phosphate ketol-isomerase, EC 5.3.1.1) deficiency is a recessive disorder that results in hemolytic anemia and neuromuscular dysfunction. To determine the molecular basis of this disorder, a TPI allele from two unrelated patients homozygous for TPI deficiency was compared with an allele from a normal individual. Each disease-associated sequence harbors a G X C----C X G transversion in the codon for amino acid-104 and specifies a structurally altered protein in which a glutamate residue is replaced by an aspartate residue. The importance of glutamate-104 to enzyme structure and function is implicated by its conservation in the TPI protein of all species that have been characterized to date. The glutamate-to-aspartate substitution results in a thermolabile enzyme as demonstrated by assays of TPI activity in cultured fibroblasts of each patient and cultured Chinese hamster ovary (CHO) cells that were stably transformed with the mutant alleles. Although this substitution conserves the overall charge of amino acid-104, the x-ray crystal structure of chicken TPI indicates that the loss of a side-chain methylene group (-CH2CH2COO- ---- -CH2COO-) is sufficient to disrupt the counterbalancing of charges that normally exists within a hydrophobic pocket of the native enzyme.

Common precursor of lysozymes of hen egg-white and bacteriophage T4

The lysozymes of hen egg-white and bacteriophage T4 have similar catalytic properties but their amino acid sequences are not homologous. The question therefore arises whether they are derived from a common ancestral protein or have arisen independently. On the basis of the data we have gathered, it is shown here that the two enzymes are similar in the conformation of their backbones, in their modes of binding substrates, in specific protein--substrate interactions and in their presumed modes of action. We conclude that the two enzymes have diverged from a common precursor. This seems to be the most convincing example to date of the divergence of proteins with nonhomologous amino acid sequences.