Independence divergence-generated binary trees of amino acids

The discovery of the relationship between amino acids is importantin terms of the replacement ability, as used in protein engineeringhomology studies, and gaining a better understanding of theroles which various properties of the residues play in the creationof a unique, stable, 3-D protein structure. Amino acid sequencesof proteins edited by evolution are anything but random. Themeasure of nonrandomness, i.e. the level of editing, can becharacterized by an independence divergence value. This parameteris used to generate binary tree relationships between aminoacids. The relationships of residues presented in this paperare based on protein building features and not on the physico-chemicalcharacteristics of amino acids. This approach is not biasedby the tautology present in all sequence similarity-based relationshipstudies. The roles which various physico-chemical characteristicsplay in the determination of the relationships between aminoacids are also discussed.     

Searching for common sequence patterns among distantly related proteins

We have developed a program Gap Allowing Pattern Explorer (GAPE)to extract amino acid sequence motifs conserved among distantlyrelated proteins. The GAPE program is designed to allow gapsin the sequences. First, this program generates all possibleamino acid patterns comprising up to five amino acids. Sequencescontaining the amino acid residues in the same order as a generatedpattern are selected as subsequences, where the differencesin the distances between two consecutive amino acids are ignored.Next, the motifs are extracted from the subsequences under conditionsin which all four distances between the five amino acids arefixed. At this stage, motifs with gaps in their subsequenceare also found by relaxing one of the four fixed distances.The statistical significance for a motif obtained is calculatedbased on the amino acid composition of the sequences under consideration.When the GAPE program was applied to 59 pyridoxal-phosphaterelatedsequences and 64 ATP (AMP-forming)-related sequences, motifsextracted with a low expectation of occurrence contained someof the amino acid residues chemically proved to be involvedin the ligand recognition.     

Local electrostatic optimization in proteins

A simple electrostatic model has been used to investigate theextent to which the structure of protein molecules is organizedto optimize the internal electrostatic interactions. We findthat the model provides a favorable total intra-protein electrostaticenergy for almost all polar and charged groups of atoms, suggestinga high degree of structural optimization. By contrast, a significantfraction of individual group–group interactions are foundto be unfavorable. An analysis as a function of the range ofinteractions included shows the electrostatic organization isgenerally relatively short range (up to 6 or 7 Å betweengroup centers). Although the model is very simple, it is usefulfor assessing the overall quality of protein experimental structures,for pin-pointing some types of errors and as a guide to improvingprotein design.     

Amino acid alphabet size in protein evolution experiments: better to search a small library thoroughly or a large library sparsely?

We compare the results obtained from searching a smaller librarythoroughly versus searching a more diverse, larger library sparsely.We study protein evolution with reduced amino acid alphabets,by simulating directed evolution experiments at three differentalphabet sizes: 20, 5 and 2. We employ a physical model forevolution, the generalized NK model, that has proved successfulin modeling protein evolution, antibody evolution and T-cellselection. We find that antibodies with higher affinity arefound by searching a library with a larger alphabet sparselythan by searching a smaller library thoroughly, even with well-designedreduced libraries. We also find ranked amino acid usage frequenciesin agreement with observations of the CDR-H3 variable regionof human antibodies.     

Predicting surface exposure of amino acids from protein sequence

The amino acid residues on a protein surface play a key rolein interaction with other molecules, determine many physicalproperties, and constrain the structure of the folded protein.A database of monomeric protein crystal structures was usedto teach computer-simulated neural networks rules for predictingsurface exposure from local sequence. These trained networksare able to correctly predict surface exposure for 72% of residuesin a testing set using a binary model (buried/exposed) and for54% of residues using a ternary model (buried/intermediate/exposed).In the ternary model, only 11% of the exposed residues are predictedas buried and only 5% of the buried residues are predicted asexposed. Also, since the networks are able to predict exposurewith a quantitative confidence estimate, it is possible to assignexposure for over half of the residues in a binary model with>80% accuracy. Even more accurate predictions are obtainedby making a consensus prediction of exposure for a homologousfamily. The effect of the local environment of an amino acidon its accessibility, though smaller than expected, is significantand accounts for the higher success rate of prediction thanobtained with previously used criteria. In the absence of athree-dimensional structure, the ability to predict surfaceaccessibility of amino acids directly from the sequence is avaluable tool in choosing sites of chemical modification orspecific mutations and in studies of molecular interaction.     

Site-directed protein recombination as a shortest-path problem

Protein function can be tuned using laboratory evolution, in which one rapidly searches through a library of proteins for the properties of interest. In site-directed recombination, n crossovers are chosen in an alignment of p parents to define a set of p(n + 1) peptide fragments. These fragments are then assembled combinatorially to create a library of p(n+1) proteins. We have developed a computational algorithm to enrich these libraries in folded proteins while maintaining an appropriate level of diversity for evolution. For a given set of parents, our algorithm selects crossovers that minimize the average energy of the library, subject to constraints on the length of each fragment. This problem is equivalent to finding the shortest path between nodes in a network, for which the global minimum can be found efficiently. Our algorithm has a running time of O(N(3)p(2) + N(2)n) for a protein of length N. Adjusting the constraints on fragment length generates a set of optimized libraries with varying degrees of diversity. By comparing these optima for different sets of parents, we rapidly determine which parents yield the lowest energy libraries.     

Concurrent mutations in six amino acids in beta-glucuronidase improve its thermostability

To achieve a thermostable beta-glucuronidase (GUS) and identify key mutation sites, we applied in vitro directed evolution strategy through DNA shuffling and obtained a highly thermostable mutant GUS gene, gus-tr, after four rounds of DNA shuffling and screening. This variant had mutations in 15 nucleic acid sites, resulting in changes in 12 amino acids (AAs). Using gus-tr as the template, we further performed site-directed mutagenesis to reverse the individual mutation to the wild-type protein. We found that six sites (Q493R, T509A, M532T, N550S, G559S and N566S) present in GUS-TR3337, were the key AAs needed to confer its high thermostability. Of these, Q493R and T509A were not reported previously as important residues for thermostability of GUS. Furthermore, all of these six mutations must be present concurrently to confer the high thermostability. We expressed the gus-tr3337 gene and purified the GUS-TR3337 protein that contained the six AA mutations. Compared with the wild-type protein which lost its activity completely after 10 min at 70 degrees C, the mutant GUS-TR3337 protein retained 75% of its activity when heated at 80 degrees C for 10 min. The GUS-TR3337 exhibited high activity even heated at 100 degrees C for 30 min on nitrocellulose filter. The comparison of molecular models of the mutated and wild-type enzyme revealed the relation of protein function and these structural modifications.     

The evolutionary landscape of functional model proteins

To study the distinct influences of structure and function onevolution, we propose a minimalist model for proteins with bindingpockets, called functional model proteins, based on a shifted-HPmodel on a two-dimensional square lattice. These model proteinsare not maximally compact and contain an empty lattice sitesurrounded by at least three nearest neighbors, thus providinga binding pocket. Functional model proteins possess a uniquenative state, cooperative folding and tolerance to mutation.Due to the explicit functionality in these models (by design),we have been able to explore their fitness or evolutionary landscapes,as characterized by the size and distribution of homologousfamilies and by the complexity of the inter-relatedness of thefunctional model proteins. Mindful that these minimalist modelsare highly idealized and two-dimensional, functional model proteinsshould nevertheless provide a useful means for exploring theconstraints of maintaining structure and function on the evolutionof proteins.     

GRAFTER: a computational aid for the design of novel proteins

The GRAFTER suite of programs provides geometric search andevaluation functions that simplify and automate the processof identifying the best scaffolds for a particular structuralmotif. Three applications of the GRAFTER suite are presented.Potential grafts between repressor and 434 repressor were identifiedthat should change the DNA binding specificity of these repressors.These results are compared with site-directed mutagenesis experimentsthat have been shown to alter repressor-DNA binding specificity.Next, 26 loops from antibody structures were grouped into familiesof similar structure. Grafts of antibody loops onto a pre-existingscaffold are an essential component of antibody humanization.Finally, interleukin (lL)-4 was searched as a scaffold thatmight accept the graft of a five residue epitope from humangrowth hormone (hGH). The existence of a crystal structure ofthe hGH-hGH receptor complex, extensive mutagenesis studiesof the hGH residues that contribute to the energetics of ligand-receptorinteractions and the gross structural homology between hGH andIL-4 make this an appealing computational target. The approachpresented here could aid the development of novel enzymes andbinding proteins     

Conservation of residue interactions in a family of Ca-binding proteins

In the TNC family of Ca-binding proteins (calmodulin, parvalbumin,intestinal calcium binding protein and troponin C) {small tilde}70 well-conserved amino acid sequences and six crystal structuresare known. We find a clear correlation between residue contactsin the structures and residue conservation in the sequences:residues with strong sidechain–sidechain contacts in thethree-dimensional structure tend to be the more conserved inthe sequence. This is one way to quantify the intuitive notionof the importance of sidechain interactions for maintainingprotein three-dimensional structure in evolution and may usefullybe taken into account in planning point mutations in proteinengineering.     

Comparison of solvent-inaccessible cores of homologous proteins: definitions useful for protein modelling

The three-dimensional structures of 41 homologous proteins (belongingto eight families) were compared by pairwise superposition.A subset of "core" residues was defined as those whose sidechains have <7% of their surface exposed to solvent. Thissubset has significantly higher sequence identity and lowerroot mean square (RMS) carbon separation than for all topologicallyequivalent residues in the structure, when members of a proteinfamily are superposed. For such superpositions the relationshipbetween RMS distance and percentage sequence identity of thissubset of residues is similar to that for all equivalent residues,although some variation is observed between families of proteinswhich are predominantly ß sheet and those which aremainly helix. The definition of a structurally more conservedcore may be ueful in model building proteins from an homologousfamily. The RMS differences of coordinates of structures ofproteins with identical sequences are found to be related tothe resolutions of the structures.     

Amino acid substitution during functionally constrained divergent evolution of protein sequences

In aligning homologous protein sequences, it is generally assumedthat amino acid substitutions subsequent in time occur independentlyof amino acid substitutions previous in time, i.e. that patternsof mulation are similar at low and high sequence divergence.This assumption is examined here and shown to be incorrect inan interesting way. Separate mutation matrices were constructedfor aligned protein sequence pairs at divergences ranging from5 to 100 PAM units (point accepted mutations per 100 alignedpositions). From these, the corresponding log-odds (Day-hoff)matrices, normalized to 250 PAM units, were constructed. Thematrices show that the genetic code influences accepted pointmutations strongly at early stages of divergence, while thechemical properties of the side chains dominate at more advancedstages.     

A single amino acid substitution can restore the solubility of aggregated colicin A mutants in Escherichia coli

Mutants of colicin A have been prepared in which the three tryptophanresidues (Trp86, Trpl30 and Trpl40), localized in the C-terminaldomain of the soluble wild-type protein, have been substitutedby phenylalanine. The Trpl40Phe single mutation had the effectof decreasing the percentage of protein that is expressed asinsoluble aggregates. The created hydrophobic cavity decreasedthe stability of the protein during its folding, resulting inpartial aggregation in the cytoplasm of the Escherichia coli-producingcells. Aggregation was increased when Trpl40 was substitutedby Lys, Leu or Cys, or if the Trpl40 mutation was combined withthe Trp86Phe and/ or Trpl30Phe mutations. A single mutation,Lysll3Phe, however, was able to restore the solubility of theaggregated mutants in vivo. Detailed analysis of the 3-D structureof the C-terminal domain of colicin A suggests that fillingof the hydrophobic cavity is responsible for this effect.     

Computer-aided gene design

A computer program, which runs on MS-DOS personal computers,is described that assists in the design of synthetic genes codingfor proteins. The goal of the program is the design of a genewhich (0 contains as many unique restriction sites as possibleand (ii) uses a specific codon usage. The gene designed accordingto the criteria above is (i) suitable for ‘modular mutagenesis’experiments and (ii) optimized for expression. The program 'reverse-translates'protein sequences into degenerated DNA sequences, generatesa map of potential restriction sites and locates sequence positionswhere unique restriction sites can be accommodated. The nucleicacid sequence is then ‘refined’ according to a specificcodon usage to remove any degeneration. Unique restriction sites,if potentially present, can be ‘forced’ into thedegenerated nucleic acid sequence by using 'priority codes'assigned to different restriction sequences.     

Automated design of degenerate codon libraries

Degenerate codon libraries are frequently used in protein engineering and evolution studies but are often limited to targeting a small number of positions to adequately limit the search space. To mitigate this, codon degeneracy can be limited using heuristics or previous knowledge of the targeted positions. To automate design of libraries given a set of amino acid sequences, an algorithm (LibDesign) was developed that generates a set of possible degenerate codon libraries, their resulting size, and their score relative to a user-defined scoring function. A gene library of a specified size can then be constructed that is representative of the given amino acid distribution or that includes specific sequences or combinations thereof. LibDesign provides a new tool for automated design of high-quality protein libraries that more effectively harness existing sequence-structure information derived from multiple sequence alignment or computational protein design data.     

A new approach to artificial and modified proteins: theory-based design, synthesis in a cell-free system and fast testing of structural properties by radiolabels

A novel approach to the creation of artificial and modifiedproteins has been elaborated. The approach includes a sequencedesign based on the molecular theory of protein secondary structureand folding patterns, gene expression in a cell-free systemand testing of structural properties of the synthesized polypeptidesat a nanogram level using radiolabelled chains. The approachhas been applied to a new synthetic protein albebetin whichhas been designed to form a 3-D fold which does not contradictany structural rule but has been never observed up to now innatural proteins. Using size-exclusion chromatography, urea-gradientelectrophoresis and limited proteolysis of a radiolabelled chain,it has been shown that the artificial protein is nearly as compactas natural proteins, cooperatively unfolds at high urea concentrationsand has some structural features of a definite structure consistentwith the designed one. As albebetin has been designed as consistingof two structural repeats, a ‘halfalbebetin’ (oneof these repeats) has also been synthesized and studied. Itwas shown that ‘half-albebetin’ is also compact     

Improved insulin stability through amino acid substitution

Insulin analogs designed to decrease self-association and increaseabsorption rates from subcutaneous tissue were found to havealtered stability. Replacement of H^B10 with aspartic acid increasedstability while substitutions at B²⁸ and/or B²⁹ were eithercomparable to insulin or had decreased stability. The principalchemical degradation product of accelerated storage conditionswas a disulfidelinked multimer that was formed through a disulfideinterchange reaction which resulted from ß-eliminationof the disulfides. The maintenance of the native state of insulinwas shown to be important in protecting the disulfides fromreduction by dithiothreitol and implicitly from the disulfideinter change reaction that occurs during storage. To understandhow these amino acid changes alter chemical stability, the intramolecularconformational equilibria of each analog was assessed by equilibriumdenaturation. The Gibbs free energy of unfolding was comparedwith the chemical stability during storage for over 20 analogs.A significant positive correla tion (R²=0.8 and P < 0.0005)exists between the conformational stability and chemical stabilityof these analogs, indicating that the chemical stability ofinsulin's disulfides is under the thermodynamic control of theconformational equilibria.     

Generation and analysis of proline mutants in protein G

The pyrrolidine ring of the amino acid proline reduces the conformational freedom of the protein backbone in its unfolded form and thus enhances protein stability. The strategy of inserting proline into regions of the protein where it does not perturb the structure has been utilized to stabilize many different proteins including enzymes. However, most of these efforts have been based on trial and error, rather than rational design. Here, we try to understand proline's effect on protein stability by introducing proline mutations into various regions of the B1 domain of Streptococcal protein G. We also applied the Optimization of Rotamers By Iterative Techniques computational protein design program, using two different solvation models, to determine the extent to which it could predict the stabilizing and destabilizing effects of prolines. Use of a surface area dependent solvation model resulted in a modest correlation between the experimental free energy of folding and computed energies; on the other hand, use of a Gaussian solvent exclusion model led to significant positive correlation. Including a backbone conformational entropy term to the computational energies increases the statistical significance of the correlation between the experimental stabilities and both solvation models.     

Hydration of amino acid side chains: dependence on secondary structure

Energy calculations have been used to study the hydration sitesaround the polar groups of serine, threonine and tyrosine sidechains. These hydration sites depend not only on the hybridizationof the polar group but also on the local secondary structure,the X₁ side chain torsion angle and the position of the hydroxylhydrogen atom. For tyrosine side chains, two solvent sites arefound approximately in the plane of the ring. Even for serineand threonine side chains only two minimum energy sites arefound in general of which one is in an expected position withinhydrogen bonding of the hydroxyl hydrogen atom (unless thisis blocked from interaction with solvent molecules by, for example,O_i–4 or O_i–3. The position of the second of thesesites depends not only on the position of the hydroxyl oxygenbut also on neighbouring main chain atoms to which it can alsohydrogen bond. There is good agreement with the solvent distributionsobtained from crystallographic data.