Changes In Binding Specificity Research Articles

Drosophila Nanos acts as a molecular clamp that modulates the RNA-binding and repression activities of Pumilio.

Collaboration among the multitude of RNA-binding proteins (RBPs) is ubiquitous, yet our understanding of these key regulatory complexes has been limited to single RBPs. We investigated combinatorial translational regulation by Drosophila Pumilio (Pum) and Nanos (Nos), which control development, fertility, and neuronal functions. Our results show how the specificity of one RBP (Pum) is modulated by cooperative RNA recognition with a second RBP (Nos) to synergistically repress mRNAs. Crystal structures of Nos-Pum-RNA complexes reveal that Nos embraces Pum and RNA, contributes sequence-specific contacts, and increases Pum RNA-binding affinity. Nos shifts the recognition sequence and promotes repression complex formation on mRNAs that are not stably bound by Pum alone, explaining the preponderance of sub-optimal Pum sites regulated in vivo. Our results illuminate the molecular mechanism of a regulatory switch controlling crucial gene expression programs, and provide a framework for understanding how the partnering of RBPs evokes changes in binding specificity that underlie regulatory network dynamics.

Structural Basis for a Switch in Receptor Binding Specificity of Two H5N1 Hemagglutinin Mutants.

Avian H5N1 influenza viruses continue to spread in wild birds and domestic poultry with sporadic infection in humans. Receptor binding specificity changes are a prerequisite for H5N1 viruses and other zoonotic viruses to be transmitted among humans. Previous reported hemagglutinin (HA) mutants from ferret-transmissible H5N1 viruses of A/Vietnam/1203/2004 and A/Indonesia/5/2005 showed slightly increased, but still very weak, binding to human receptors. From mutagenesis and glycan array studies, we previously identified two H5N1 HA mutants that could more effectively switch receptor specificity to human-like α2-6-linked sialosides with avidity comparable to wild-type H5 HA binding to avian-like α2-3-linked sialosides. Here, crystal structures of these two H5 HA mutants free and in complex with human and avian glycan receptor analogs reveal the structural basis for their preferential binding to human receptors. These findings suggest continuous surveillance should be maintained to monitor and assess human-to-human transmission potential of H5N1 viruses.

Evolution of the SH3 Domain Specificity Landscape in Yeasts.

To explore the conservation of Src homology 3 (SH3) domain-mediated networks in evolution, we compared the specificity landscape of these domains among four yeast species, Saccharomyces cerevisiae, Ashbya gossypii, Candida albicans, and Schizosaccharomyces pombe, encompassing 400 million years of evolution. We first aligned and catalogued the families of SH3-containing proteins in these four species to determine the relationships between homologous domains. Then, we tagged and purified all soluble SH3 domains (82 in total) to perform a quantitative peptide assay (SPOT) for each SH3 domain. All SPOT readouts were hierarchically clustered and we observed that the organization of the SH3 specificity landscape in three distinct profile classes remains conserved across these four yeast species. We also produced a specificity profile for each SH3 domain from manually aligned top SPOT hits and compared the within-family binding motif consensus. This analysis revealed a striking example of binding motif divergence in a C. albicans Rvs167 paralog, which cannot be explained by overall SH3 sequence or interface residue divergence, and we validated this specificity change with a yeast two-hybrid (Y2H) assay. In addition, we show that position-weighted matrices (PWM) compiled from SPOT assays can be used for binding motif screening in potential binding partners and present cases where motifs are either conserved or lost among homologous SH3 interacting proteins. Finally, by comparing pairwise SH3 sequence identity to binding profile correlation we show that for ~75% of all analyzed families the SH3 specificity profile was remarkably conserved over a large evolutionary distance. Thus, a high sequence identity within an SH3 domain family predicts conserved binding specificity, whereas divergence in sequence identity often coincided with a change in binding specificity within this family. As such, our results are important for future studies aimed at unraveling complex specificity networks of peptide recognition domains in higher eukaryotes, including mammals.

Protein engineering in the 21st century.

Protein engineering, the process by which novel proteins with desired properties are developed, has grown by leaps and bounds since the first examples of protein mutagenesis were described over three decades ago. In the last 30 years, protein engineers have successfully created a wide range of proteins tailored to specific industrial, medical, and research applications. Yet challenges remain that prevent the engineering of complex protein functions on demand. With the aim of creating a forum for the protein engineering community, the inaugural Protein Engineering Canada Conference was held on June 20–22, 2014, in Ottawa, Canada. Over the course of the 2-day conference, 115 protein scientists from over 30 institutions representing 5 countries shared ideas, networked with colleagues, and learned about exciting new research covering a broad array of topics such as enzyme engineering, computational protein design, X-ray crystallography, protein NMR, molecular modeling, and protein evolution. This special issue highlights the breadth of research that was covered during the Protein Engineering Canada Conference by including previously unpublished research articles submitted by speakers as well as some selections that were submitted directly to Protein Science.

Human-specific evolutionary changes in the biology of siglecs.

Siglecs are a family of sialic acid-recognizing immunoglobulin-like lectins that exhibit multiple human-specific and human-universal differences, including changes in binding specificity (Siglec-5, -7, -9, -11, -12 and 14); changes in expression pattern (Siglec-1, -5, -6, and -11); gene conversion (SIGLEC11); gene deletion (SIGLEC13) and pseudogenization (SIGLEC17). Human-unique pseudogenes of SIGLEC12, SIGLEC14 and SIGLEC16 are also polymorphic within human populations, suggesting ongoing selection on this family of genes. The apparently higher concentration of SIGLEC changes in the human lineage may have been selected by interactions with pathogens binding Siglecs, and/or as compensatory responses to the loss of the sialic acid N-glycolylneuraminic acid (Neu5Gc) in humans. Human-specific Siglec changes of particular interest include expression of Siglec-11 in brain microglia, expression of Siglec-6 on placental trophoblast, suppression of Siglec-5 expression on adaptive immune cells, new expression of Siglec-5 on amniotic epithelium, and elimination of Siglec-13 and -17 from innate immune cells. The Siglec-13 and -17 inactivation events fixed in the ancestral population shortly before the common ancestor of modern humans 100–200 thousand years ago, and resurrected Siglec-13 and -17 gene products bind potentially lethal pathogens of infants. While such pathogens may have contributed to population bottlenecks in human evolution, the resulting changes in sialic acid biology may also have altered multiple systems where sialic acid and Siglecs have endogenous roles. Thus, genes associated with sialic acid biology appear to be a “hot spot” of genetic and physiological change during human evolution, with implications for human origins, and for uniquely human features in health and disease.

Insights into the binding specificity of wild type and mutated wheat germ agglutinin towards Neu5Acα(2‐3)Gal: a study by in silico mutations and molecular dynamics simulations

Wheat germ agglutinin (WGA) is a plant lectin, which specifically recognizes the sugars NeuNAc and GlcNAc. Mutated WGA with enhanced binding specificity can be used as biomarkers for cancer. In silico mutations are performed at the active site of WGA to enhance the binding specificity towards sialylglycans, and molecular dynamics simulations of 20 ns are carried out for wild type and mutated WGAs (WGA1, WGA2, and WGA3) in complex with sialylgalactose to examine the change in binding specificity. MD simulations reveal the change in binding specificity of wild type and mutated WGAs towards sialylgalactose and bound conformational flexibility of sialylgalactose. The mutated polar amino acid residues Asn114 (S114N), Lys118 (G118K), and Arg118 (G118R) make direct and water mediated hydrogen bonds and hydrophobic interactions with sialylgalactose. An analysis of possible hydrogen bonds, hydrophobic interactions, total pair wise interaction energy between active site residues and sialylgalactose and MM-PBSA free energy calculation reveals the plausible binding modes and the role of water in stabilizing different binding modes. An interesting observation is that the binding specificity of mutated WGAs (cyborg lectin) towards sialylgalactose is found to be higher in double point mutation (WGA3). One of the substituted residues Arg118 plays a crucial role in sugar binding. Based on the interactions and energy calculations, it is concluded that the order of binding specificity of WGAs towards sialylgalactose is WGA3 > WGA1 > WGA2 > WGA. On comparing with the wild type, double point mutated WGA (WGA3) exhibits increased specificity towards sialylgalactose, and thus, it can be effectively used in targeted drug delivery and as biological cell marker in cancer therapeutics.

The Haemophilus Cryptic Genospecies Cha Adhesin Has at Least Two Variants That Differ in Host Cell Binding, Bacterial Aggregation, and Biofilm Formation Properties

The Haemophilus cryptic genospecies (HCG) causes genital tract infections in pregnant and postpartum women and respiratory infections in neonates. The major surface adhesin in HCG is called Cha, which mediates bacterial adherence to cultured human epithelial cells. In this study, we report that there are two antigenically distinct variants of Cha, dubbed Cha1 and Cha2. These variants are encoded by the same genetic locus in diverse strains and have nearly identical N-terminal export and C-terminal surface anchoring domains but significantly different internal adhesive domains. Based on the comparison of derivatives of a laboratory strain of Haemophilus influenzae expressing either surface-associated Cha1 or surface-associated Cha2, Cha1 mediates a higher level of adherence to cultured human epithelial cells and Cha2 mediates a higher level of adherence to abiotic surfaces. We hypothesize that variation in the Cha1 and Cha2 internal region results in changes in binding specificity or binding affinity and may be associated with adaptation to different host environments during colonization and disease.

The role of protein sequence and global conformation in DNA binding specificity of members of the Cro family

The Cro family of bacteriophage DNA‐binding proteins demonstrates the substantial conformational changes that can occur in protein evolution while the primary sequence is significantly conserved. Xfaso 1 and Pfl 6 of the Cro family are α‐helical and mixed α‐helical/β‐sheet, respectively, despite sharing 40% sequence identity. Both proteins are transcription factors that use a helix‐turn‐helix (HTH) motif as their primary DNA recognition moiety. However, the natural consensus DNA sequences of the proteins are different at three positions in each seven base‐pair half site. Fluorescence anisotropy measurements showed that wild‐type (WT) Xfaso 1 and Pfl 6 bound their cognate sites with dissociation constants (KD) of 230 nM and 56 nM, respectively. WT Pfl 6 bound its noncognate site with KD = 1.99 μM and WT Xfaso 1 did not bind its noncognate site at all. To explore whether this change in binding specificity is due to differences in sequence in the HTH region or to global differences in their tertiary structures, mutations were introduced into the HTH region of both proteins in order to equalize the binding region sequence while retaining global structure. The binding affinities of these variant proteins against the consensus binding sites were tested and preliminary results suggest that mutation of the Xfaso 1 sequence toward Pfl 6 allows it to bind the Pfl 6 consensus site. Funded by NSF (MCB‐0647390) and HHMI (52005889).

Coordinated Genome-Wide Modifications within Proximal Promoter Cis-regulatory Elements during Vertebrate Evolution

There often exists a “one-to-many” relationship between a transcription factor and a multitude of binding sites throughout the genome. It is commonly assumed that transcription factor binding motifs remain largely static over the course of evolution because changes in binding specificity can alter the interactions with potentially hundreds of sites across the genome. Focusing on regulatory motifs overrepresented at specific locations within or near the promoter, we find that a surprisingly large number of cis-regulatory elements have been subject to coordinated genome-wide modifications during vertebrate evolution, such that the motif frequency changes on a single branch of vertebrate phylogeny. This was found to be the case even between closely related mammal species, with nearly a third of all location-specific consensus motifs exhibiting significant modifications within the human or mouse lineage since their divergence. Many of these modifications are likely to be compensatory changes throughout the genome following changes in protein factor binding affinities, whereas others may be due to changes in mutation rates or effective population size. The likelihood that this happened many times during vertebrate evolution highlights the need to examine additional taxa and to understand the evolutionary and molecular mechanisms underlying the evolution of protein–DNA interactions.

Uniquely human evolution of sialic acid genetics and biology

Darwinian evolution of humans from our common ancestors with nonhuman primates involved many gene-environment interactions at the population level, and the resulting human-specific genetic changes must contribute to the "Human Condition." Recent data indicate that the biology of sialic acids (which directly involves less than 60 genes) shows more than 10 uniquely human genetic changes in comparison with our closest evolutionary relatives. Known outcomes are tissue-specific changes in abundant cell-surface glycans, changes in specificity and/or expression of multiple proteins that recognize these glycans, and novel pathogen regimes. Specific events include Alu-mediated inactivation of the CMAH gene, resulting in loss of synthesis of the Sia N-glycolylneuraminic acid (Neu5Gc) and increase in expression of the precursor N-acetylneuraminic acid (Neu5Ac); increased expression of alpha2-6-linked Sias (likely because of changed expression of ST6GALI); and multiple changes in SIGLEC genes encoding Sia-recognizing Ig-like lectins (Siglecs). The last includes binding specificity changes (in Siglecs -5, -7, -9, -11, and -12); expression pattern changes (in Siglecs -1, -5, -6, and -11); gene conversion (SIGLEC11); and deletion or pseudogenization (SIGLEC13, SIGLEC14, and SIGLEC16). A nongenetic outcome of the CMAH mutation is human metabolic incorporation of foreign dietary Neu5Gc, in the face of circulating anti-Neu5Gc antibodies, generating a novel "xeno-auto-antigen" situation. Taken together, these data suggest that both the genes associated with Sia biology and the related impacts of the environment comprise a relative "hot spot" of genetic and physiological changes in human evolution, with implications for uniquely human features both in health and disease.

An investigation into the relationship between calmodulin protein conformation and binding specificity

In the presence of calcium, calmodulin (CaM) undergoes large conformational changes throughout the protein to present a structurally dynamic surface that can recognize and bind numerous target proteins to transduce the cell's calcium signal. Most of these structural changes occur in the protein's unique central linker region, which serves as a molecular hinge between the N‐ and C‐terminal dual EF‐hand calcium binding domains. Numerous studies have led to the hypothesis that the interactions provided by this region are primarily responsible for CaM‐target binding affinity and thus, CaM's binding specificity. To further examine the relationship between protein sequence, conformation, and CaM's pluripotent binding specificity, we constructed linker‐region protein libraries designed to differentially restrict the conformational freedom of the molecule. Individual, non‐selected library members were characterized by circular dichroism spectroscopy to investigate alterations in conformational change upon calcium binding, and fluorescence binding studies with CaM‐peptide targets to investigate changes in binding specificity. We present the initial structural and binding characterization of these randomly selected library proteins.

Theoretical analysis of binding specificity of influenza viral hemagglutinin to avian and human receptors based on the fragment molecular orbital method

The hemagglutinin (HA) protein of the influenza virus binds to the host cell receptor in the early stage of viral infection. A change in binding specificity from avian α2–3 to human α2–6 receptor is essential for optimal human-to-human transmission and pandemics. Therefore, it is important to reveal the key factors governing the binding affinity of HA-receptor complex at the molecular level for the understanding and prediction of influenza pandemics. In this work, on the basis of ab initio fragment molecular orbital (FMO) method, we have carried out the interaction energy analysis of HA-receptor complexes to quantitatively elucidate the binding specificity of HAs to avian and human receptors. To discuss the binding property of influenza HA comprehensively, a number of HAs from human H1, swine H1, avian H3 and avian H5 viruses were analyzed. We performed detailed investigations about the interaction patterns of complexes of various HAs and receptor analogues, and revealed that intra-molecular interactions between conserved residues in HA play an important role for HA-receptor binding. These results may provide a hint to understand the role of conserved acidic residues at the receptor binding site which are destabilized by the electrostatic repulsion with sialic acid. The calculated binding energies and interaction patterns between receptor and HAs are consistent with the binding specificities of each HA and thus explain the receptor binding mechanism. The calculated results in the present analysis have provided a number of viewpoints regarding the models for the HA-receptor binding specificity associated with mutated residues. Examples include the role of Glu190 and Gln226 for the binding specificity of H5 HA. Since H5 HA has not yet been adapted to human receptor and the mechanism of the specificity change is unknown, this result is helpful for the prediction of the change in receptor specificity associated with forthcoming possible pandemics.

Convergent and Divergent Ligand Specificity among PDZ Domains of the LAP and Zonula Occludens (ZO) Families

We present a detailed comparative analysis of the PDZ domains of the human LAP proteins Erbin, Densin-180, and Scribble and the MAGUK ZO-1. Phage-displayed peptide libraries and in vitro affinity assays were used to define ligand binding profiles for each domain. The analysis reveals the importance of interactions with all four C-terminal residues of the ligand, which constitute a core recognition motif, and also the role of interactions with more upstream ligand residues that support and modulate the core binding interaction. In particular, the results highlight the importance of site(-1), which interacts with the penultimate residue of ligand C termini. Site(-1) was found to be monospecific in the Erbin PDZ domain (accepts tryptophan only), bispecific in the first PDZ domain of ZO-1 (accepts tryptophan or tyrosine), and promiscuous in the Scribble PDZ domains. Furthermore, it appears that the level of promiscuity within site(-1) greatly influences the range of potential biological partners and functions that can be associated with each protein. These findings show that subtle changes in binding specificity can significantly alter the range of biological partners for PDZ domains, and the insights enhance our understanding of this diverse family of peptide-binding modules.

Determinants of Binding Affinity and Specificity for the Interaction of TEM-1 and SME-1 β-Lactamase with β-Lactamase Inhibitory Protein

The hydrolysis of beta-lactam antibiotics by class A beta-lactamases is a common cause of bacterial resistance to these agents. The beta-lactamase inhibitory protein (BLIP) is able to bind and inhibit several class A beta-lactamases, including TEM-1 beta-lactamase and SME-1 beta-lactamase. Although the TEM-1 and SME-1 enzymes share 33% amino acid sequence identity and a similar fold, they differ substantially in surface electrostatic properties and the conformation of a loop-helix region that BLIP binds. Alanine-scanning mutagenesis was performed to identify the residues on BLIP that contribute to its binding affinity for each of these enzymes. The results indicate that the sequence requirements for binding are similar for both enzymes with most of the binding free energy provided by two patches of aromatic residues on the surface of BLIP. Polar residues such as several serines in the interface do not make significant contributions to affinity for either enzyme. In addition, the specificity of binding is significantly altered by mutation of two charged residues, Glu73 and Lys74, that are buried in the structure of the TEM-1.BLIP complex as well as by residues located on two loops that insert into the active site pocket. Based on the results, a E73A/Y50A double mutant was constructed that exhibited a 220,000-fold change in binding specificity for the TEM-1 versus SME-1 enzymes.

Calculation of the pKa values for the ligands and side chains of Escherichia coli D-alanine:D-alanine ligase.

Poisson-Boltzmann electrostatics methods have been used to calculate the pKa shifts for the ligands and titratable side chains of D-alanine:D-alanine ligase of the ddlb gene of Escherichia coli (DdlB). The focus of this study is to determine the ionization state of the second D-alanine (D-Ala2) in the active site of DdlB. The pKa of the amine is shifted over 5 pKa units more alkaline in the protein, clearly implying that D-Ala2 is bound to DdlB in its zwitterionic state and not in the free-base form as had been previously suggested. Comparisons are made to the depsipeptide ligase from the vancomycin-resistance cascade, VanA. It is suggested that VanA has different enzymatic properties due to a change in binding specificity rather than altered catalytic behavior and that the specificity of binding D-lactate over D-Ala2 may arise from the difference in ionization characteristics of the ligands.

Mutants of rat intestinal fatty acid-binding protein illustrate the critical role played by enthalpy-entropy compensation in ligand binding.

Site-specific variants of rat intestinal fatty acid-binding protein were constructed to identify the molecular interactions that are important for binding to fatty acids (FAs). Several variants displayed affinities that appeared incompatible with the crystal structure of the protein-FA complex. Thermodynamic measurements provided an explanation for these apparent inconsistencies and revealed that binding affinities often inaccurately reported changes in protein-FA interactions because changes in the binding entropy and enthalpy were usually compensatory. These results demonstrate that understanding the effects of amino acid replacements on ligand binding requires measurements of enthalpy and entropy, in addition to affinity.

Acidic pH changes receptor binding specificity of Helicobacter pylori: a binary adhesion model in which surface heat shock (stress) proteins mediate sulfatide recognition in gastric colonization.

The gastric pathogen helicobacter pylori is one of a number of bacteria which bind specifically to gangliotetraosylceramide, gangliotriaosylceramide, and phosphatidylethanolamine in vitro at neutral pH. Since this organism encounters an acid pH during initial infection of the stomach, we have monitored the effect of pH on receptor binding specificity and found induction of specific binding to sulfoglycolipids (sulfatide) following brief treatment at low pH. We have previously shown that heat shock proteins (hsps) bind to sulfatide, and the suspicion that this was a stress-induced response is supported by the fact that a similar change in H. pylori binding specificity was observed if the organisms were briefly exposed to heat shock treatment. Following the stress stimulus, the change in glycolipid binding specificity was prevented by the inclusion of inhibitors of protein synthesis or by incubation with anti-hsp antibodies. Expression of hsps in the surface extract and surface reactivity with anti-hsp antibodies correlated with the change in glycolipid binding specificity. Despite the presence of high levels of H. pylori cell surface urease activity which may neutralize the microenvironmental pH, the acid-induced change in binding specificity was enhanced in the presence of urea. These studies suggest that cell surface hsps mediate sulfatide recognition by this organism under stress conditions. A binary receptor model is proposed for gastric colonization by H. pylori.

Inhibition of Bovine Brain Nitric-Oxide Synthase by α-Amino and α-Carboxyl Derivatives of NG-Allyl-L-Arginine

Three derivatives of the mechanism-based inhibitor N G-allyl-L-arginine, designed to eliminate the effect of charge on the α-functional groups, were synthesized and tested as inhibitors of purified bovine brain nitric oxide synthase. The inhibitory properties of N G-allyl-L-arginine, N G-allyl-L-arginine methyl ester, N α-acetyl- N G-allyl-L-arginine, and N α-acetyl- N G-allyl-L-arginine methyl ester were determined in steady-state kinetic assays. The K i s of the four compounds were 7 ± 1, 11 ± 1, 147 ± 13, and 480 ± 45 μM, respectively. These results demonstrate that conversion of the α-carboxylgroup of N G-allyl-L-arginine to a methyl ester had only a small effect on its inhibitory properties, whereas acetylation of the α-amino group increased the K i by more than an order of magnitude. Modification of both the α-amino and α-carboxyl groups increased the K i more dramatically from 7 to 480 μM. Derivatization of the α-amino and α-carboxyl groups of N G-allyl-L-arginine would not be expected to alter the chemistry of inactivation by the N G-allyl guanidine moiety, and therefore the increased K i s of the derivatives are probably due solely to changes in binding specificity. These data suggest that the arginine binding pocket of brain nitric oxide synthase prefers the unmodified α-amino group of arginine for binding, but that it can accommodate a modified α-carboxylate. Thus, conservative modification at the alpha-carboxyl may represent a starting point for the design and synthesis of other inhibitors targeted at nitric oxide synthase.

A High Affinity Digoxin-binding Protein Displayed on M13 Is Functionally Identical to the Native Protein

Phage display of peptides and proteins has successfully been employed to produce binding molecules of altered affinity. Little is known, however, regarding the impact on affinity measurements of phage-displayed molecules compared to their native freely soluble configuration. That identical affinities can be obtained was shown by Scatchard analysis of the native antibody, its single chain derivative (scFv), and its phage-displayed single chain counterpart for the ligand digoxin. No significant difference, within one standard deviation, was detected in affinity for digoxin when the phage-displayed scFv was compared to either its soluble scFv form or the purified antibody. In addition, no change in binding specificity was detected, within two standard deviations, when the binding proteins were challenged with two commonly cross-reactive compounds (dihydrodigoxin and digitoxin). That phage-display can be employed for molecules having high binding affinities (Kd of 6 x 10(-11) M) is also shown.

Alpha-fetoprotein: the major high-affinity estrogen binder in rat uterine cytosols.

Evidence is present that alpha-fetoprotein (AFP), a serum globulin, accounts mainly, if not entirely, for the high estrogen-binding properties of uterine cytosols from immature rats. By the use of specific immunoadsorbents to AFP and by competitive assays with unlabeled steroids and pure AFP, it has been demonstrated that in hypotonic cytosols AFP is present partly as free protein with a sedimentation coefficient of about 4-5 S and partly in association with some intracellular constituent(s) to form an 8S estrogen-binding entity. The AFP leads to 8S transformation results in a loss of antigenic reactivity to antibodies against AFP and a significant change in binding specificity. This change in binding specificity is manifested by an increase in binding affinity for estradiol, estriol, diethylstillbestrol, and nafoxidine ( a non-steroidal anti-estrogen), and by a concomitant decrease in estrone binding. Both the antigenic and binding properties of native AFP are recovered after dissociation of the 8S complex in 0.4 M KC1. An AFP-mediated mechanism of early intracellular events associated with estrogen entry in target cells is suggested and discussed with regard to current views on steroid action.