Role Of Conformational Flexibility Research Articles

Investigation of crystal structures, energetics and isostructurality in halogen-substituted phosphoramidates

A total of 14 compounds, one unsubstituted and 13 halogen-substituted phosphoramidates, have been synthesized from unsubstituted and halogenated (fluoro-, difluoro-, chloro-, bromo-, iodo-substituted) aniline and diphenyl phosphoryl chloride to investigate their molecular assembly in solid-state structures. Amongst them, six groups were formed based on similarities in unit-cell dimensions, space group and molecular assembly of the crystal. The analysis reveals that all the crystal structures contain robust N-H...O hydrogen bonds which are the primary building blocks with ancillary interactions such as C-H...O, C-H...π, C-H...F/Cl/Br/I, F...F, F...π, I...π, Br...π, I...O and Br...O. The role of short and directional C-H...O and C-H...π interactions providing significant stabilization to the densely packed crystalline arrangement is discussed. The contribution of these interactions in stabilizing the crystalline assembly was deduced via computing total interaction energy between dimers and the overall lattice energies using the computer programs CrystalExplorer17.5 and PIXELC, respectively. Additionally, the occurrence of 3D isostructurality in phosphoradimates and their halogenated analogs was investigated using the XPac program. A comparison of the magnitudes of the torsion angles in the compounds substantiates the role of conformational flexibility in the solid state.

Role of Conformational Flexibility in Monte Carlo Simulations of Many-Protein Systems.

Efficient computational modeling of biological systems characterized by high concentrations of macromolecules often relies on rigid-body Brownian Dynamics or Monte Carlo (MC) simulations. However, the accuracy of rigid-body models is limited by the fixed conformation of the simulated biomolecules. Multi-conformation Monte Carlo (mcMC) simulations of protein solutions incorporate conformational flexibility via a conformational swap trial move within a predetermined library of discrete protein structures, thereby alleviating artifacts arising from the use of a single protein conformation. Here, we investigate the impact of the number of distinct protein structures in the conformational library and the extent of conformational sampling used in its generation on structural observables computed from simulations of hen egg white lysozyme (HEWL), human γD-Crystallin, and bovine γB-Crystallin solutions. We find that the importance of specific protocols for the construction of the protein structure library is strongly dependent on the nature of the simulated system.

Previously Hidden Dynamics at the TCR–Peptide–MHC Interface Revealed

A structural characterization of the interaction between αβ TCRs and cognate peptide-MHC (pMHC) is central to understanding adaptive T cell-mediated immunity. X-ray crystallography, although the source of much structural data, traditionally provides only a static snapshot of the protein. Given the emerging evidence for the important role of conformational dynamics in protein function, we interrogated 309 crystallographic structures of pMHC complexes using ensemble refinement, a technique that can extract dynamic information from the x-ray data. Focusing on a subset of human pMHC class I systems, we found that in many cases, ensemble methods were able to uncover previously hidden evidence of significant conformational plasticity, thereby revealing additional information that can build upon and significantly enhance functional interpretations that are based on a single static structure. Notable examples include the interpretation of differences in the disease association of HLA subtypes, the relationship between peptide prominence and TCR recognition, the role of conformational flexibility in vaccine design, and the discrimination between induced fit and conformational selection models of TCR binding. We show that the currently widespread practice of analyzing pMHC interactions via the study of a single crystallographic structure does not make use of pertinent and easily accessible information from x-ray data concerning alternative protein conformations. This new analysis therefore not only highlights the capacity for ensemble methods to significantly enrich the interpretation of decades of structural data but also provides previously missing information concerning the dynamics of existing characterized TCR-pMHC interactions.

Transferase Versus Hydrolase: The Role of Conformational Flexibility in Reaction Specificity

Active in the aqueous cellular environment where a massive excess of water is perpetually present, enzymes that catalyze the transfer of an electrophile to a non-water nucleophile (transferases) require specific strategies to inhibit mechanistically related hydrolysis reactions. To identify principles that confer transferase versus hydrolase reaction specificity, we exploited two enzymes that use highly similar catalytic apparatuses to catalyze the transglycosylation (a transferase reaction) or hydrolysis of α-1,3-glucan linkages in the cyclic tetrasaccharide cycloalternan (CA). We show that substrate binding to non-catalytic domains and a conformationally stable active site promote CA transglycosylation, whereas a distinct pattern of active site conformational change is associated with CA hydrolysis. These findings defy the classic view of induced-fit conformational change and illustrate a mechanism by which a stable hydrophobic binding site can favor transferase activity and disfavor hydrolysis. Application of these principles could facilitate the rational reengineering of transferases with desired catalytic properties.

'Dual' peptidyl-oligonucleotide conjugates: Role of conformational flexibility in catalytic cleavage of RNA.

Traditional therapeutic interventions against abnormal gene expression in disease states at the level of expressed proteins are becoming increasingly difficult due to poor selectivity, off-target effects and associated toxicity. Upstream catalytic targeting of specific RNA sequences offers an alternative platform for drug discovery to achieve more potent and selective treatment through antisense interference with disease-relevant RNAs. We report a novel class of catalytic biomaterials, comprising amphipathic RNA-cleaving peptides placed between two RNA recognition motifs, here demonstrated to target the TΨC loop and 3'- acceptor stem of tRNAPhe. These unique peptidyl-oligonucleotide 'dual' conjugates (DCs) were created by phosphoramidate or thiol-maleimide conjugation chemistry of a TΨC-targeting oligonucleotide to the N-terminus of the amphipathic peptide sequence, followed by amide coupling of a 3'-acceptor stem-targeting oligonucleotide to the free C-terminal carboxylic acid functionality of the same peptide. Hybridization of the DCs bearing two spatially-separated recognition motifs with the target tRNAPhe placed the peptide adjacent to a single-stranded RNA region and promoted cleavage within the 'action radius' of the catalytic peptide. Up to 100% cleavage of the target tRNAPhe was achieved by the best candidate (i.e. DC6) within 4h, when conformational flexibility was introduced into the linker regions between the peptide and oligonucleotide components. This study provides the strong position for future development of highly selective RNA-targeting agents that can potentially be used for disease-selective treatment at the level of messenger, micro, and genomic viral RNA.

The role of conformational flexibility in Baeyer-Villiger monooxygenase catalysis and structure

BackgroundThe Baeyer-Villiger monooxygenases (BMVOs) are a group of microbial enzymes that have garnered interest as industrial biocatalysts. While great strides have been made in recent years to understand the mechanism of these enzymes from a structural perspective, our understanding remains incomplete. In particular, the role of a twenty residue loop (residues 487–504), which we refer to as the “Control Loop,” that is observed in either an ordered or disordered state in various crystal structures remains unclear. MethodsUsing SAXS, we have made the first observations of the Loop in solution with two BVMOs, cyclohexanone monooxygenase (CHMO) and cyclopentadecanone monooxygenase. We also made a series of mutants of CHMO and analyzed them using SAXS, ITC, and an uncoupling assay. ResultsThese experiments show that Control Loop ordering results in an overall more compact enzyme without altering global protein foldedness. We have also demonstrated that the Loop plays a critical and complex role on enzyme structure and catalysis. The Control Loop appears to have a direct impact on the organization of the overall structure of the protein, as well as in influencing the active site environment. ConclusionsThe data imply that the Loop can be divided into two regions, referred to as “sub-loops,” that coordinate overall domain movements to changes in the active site. General significanceA better understanding of the mechanistic role of the Control Loop may ultimately be helpful in designing mutants with altered specificity and improved catalytic efficiency.

Evolution of Metal Ion and Purine Nucleotide Effects and Cooperativity in Glutamate Dehydrogenase: The Role of Conformational Flexibility

Higher eukaryote glutamate dehydrogenases are highly allosterically regulated by a wide variety of compounds including purine nucleotides and metal ions. Of the purine nucleotides ADP and GTP are the most potent allosteric heterotropic effectors while NAD(P)+ shows negative homotropic allosteric effects involving communication between active sites. To investigate potential evolutionary factors we have compared a variety of available structures and homology models of glutamate dehydrogenases that either show allosteric effects or lack allosteric interactions to elucidate the formation of either the purine heterotropic sites or the metal binding sites of the enzyme using HINT computational analysis of contributions to binding. Local Spatial Pattern alignments have identified potential conformationally flexible spines that could form pathways of conformational changes. The effects of purine nucleotides and various metal ions on overall stability have been determined by both heat and chemical denaturation using CD and fluorescence spectroscopy. Inhibition is correlated with decreased flexibility while activators enhance flexibility. Similar studies with inhibitory or non‐inhibitory meal ions and limited proteolysis experiments using immobilized trypsin and tandem mass spectrometry to identify initial cleavage sites provide more detailed spatial information are in progress.

Affinity and Selectivity of Peptides for Inorganic Materials: A Thermodynamic Discussion of the Role of Conformational Flexibility

The recognition of inorganic materials by polypeptides is a technologically relevant and scientifically intriguing phenomenon. Several features of the polypeptide determine the affinity for a given surface and, possibly, its selectivity among a set of materials or among various crystal planes of the same material. Different amino acids have different intrinsic affinities for a given surface; the geometrical features of the surface are also relevant in the recognition process. By means of a minimal, analytically solvable thermodynamic model for the polypeptide-surface interaction, we discuss the role of the conformational flexibility in determining affinity and selectivity of polypeptides for surfaces. In particular, the interplay between geometrical matching of polypeptide-surface features and the presence in the polypeptide of amino acids able to bind the target surface is analyzed as a function of the flexibility. A discussion of literature data in the light of this minimal model is also given.

Regulating the architectures of hydrogen-bonded frameworks through topological enforcement.

The role of conformational flexibility in topological enforcement of several crystalline materials based on hydrogen-bonded two-dimensional guanidinium-sulfonate (GS) networks is demonstrated by using a series of organopolysulfonates that prompt the formation of either lamellar or cylindrical architectures. Whereas flexible organopolysulfonate linkers decorated with flexible arms self-assemble into lamellar architectures, rigid organopolysulfonates linkers enforce the formation of hydrogen-bonded cylinders with intercylinder spacing governed by the size of the linker. Specifically, hexagonal cylindrical structures generated from trisulfonates with three-fold molecular symmetry are the topological equivalent of the cylindrical hexagonal phases reported previously for guanidinium organomonosulfonate inclusion compounds, but neighboring cylinders are now connected through covalent nodes provided by the trisulfonates rather than dispersive interactions between the arene rings of the organomonosulfonates. Organopolysulfonates with moderate conformational freedom, however, can generate both lamellar and cylindrical structures, depending on the guest molecules encapsulated by the host framework. These observations illustrate that the crystal architecture (i.e., lamellar vs cylindrical) and the shape of GS cylinders can be regulated in a predictable way by the molecular symmetries and conformational constraints of the organopolysulfonates building blocks.

Dynamic adsorption and dilatational properties of BSA at oil/water interface: Role of conformational flexibility

The influence of protein concentration (c) and/or disulfide bond (S–S) cleavage with β-mercaptoethanol (2-ME) on interfacial adsorption dynamics, including diffusion, penetration and structural rearrangement at the interface, as well as dynamic dilatational properties of bovine serum albumin (BSA) was systematically investigated using drop shape analysis. The results indicated that for native BSA increasing the c from 0.01 to 0.5% (w/v) progressively improved the rate of diffusion and the ‘equilibrium’ surface pressure (π), while a further increase in c (to 1.0%, w/v) contrarily impaired these characteristics; increasing the c progressively improved the penetration and structural rearrangement at the interface. In contrast, the surface dilatational modulus (E) development was less dependent on the c than that for the π. On the other hand, the S–S cleavage with 2-ME at any test c value progressively improved the diffusion and penetration, as well as ‘equilibrium’ π, while the structural rearrangement was highly dependent on the c. At c < 0.5% (w/v), increasing the 2-ME concentration progressively improved the rearrangement, while at c values of 0.5% or above, a contrary trend was observed. The S–S cleavage generally improved the E or its elasticity development over the whole adsorption, regardless of the c. The E-π plots indicated that besides the adsorption, the lateral macromolecular interactions at the interface could be affected by variation in c and/or 2-ME concentration. The relationships between the conformational flexibility and interfacial characteristics of BSA, as well as between its interfacial and emulsifying properties have been well established.

Diverse modes of binding in structures of Leishmania major N-myristoyltransferase with selective inhibitors.

The leishmaniases are a spectrum of global diseases of poverty associated with immune dysfunction and are the cause of high morbidity. Despite the long history of these diseases, no effective vaccine is available and the currently used drugs are variously compromised by moderate efficacy, complex side effects and the emergence of resistance. It is therefore widely accepted that new therapies are needed. N-Myristoyltransferase (NMT) has been validated pre-clinically as a target for the treatment of fungal and parasitic infections. In a previously reported high-throughput screening program, a number of hit compounds with activity against NMT from Leishmania donovani have been identified. Here, high-resolution crystal structures of representative compounds from four hit series in ternary complexes with myristoyl-CoA and NMT from the closely related L. major are reported. The structures reveal that the inhibitors associate with the peptide-binding groove at a site adjacent to the bound myristoyl-CoA and the catalytic α-carboxylate of Leu421. Each inhibitor makes extensive apolar contacts as well as a small number of polar contacts with the protein. Remarkably, the compounds exploit different features of the peptide-binding groove and collectively occupy a substantial volume of this pocket, suggesting that there is potential for the design of chimaeric inhibitors with significantly enhanced binding. Despite the high conservation of the active sites of the parasite and human NMTs, the inhibitors act selectively over the host enzyme. The role of conformational flexibility in the side chain of Tyr217 in conferring selectivity is discussed.

The Role of Conformational Flexibility in Inhibitor Binding and Substrate Recognition for Cyp119

Conformational flexibility of several cytochromes P450 has been observed in response to substrate and ligand binding, and thus may play an important role in catalysis. CYP119, a bacterial thermophilic protein from cytochrome P450 superfamily has been observed in three different conformations with different inhibitors bound using X-ray crystallography, but the significance of these states in solution and in the function of the enzyme is not well known. According to the crystal structures, much of the diversity in conformational states arises in F and G helices, which fold around the substrate binding site at the distal heme face. Double electron electron resonance (DEER) was used to measure the average distances and the distance distributions between spin-labels for populated conformational states in solution. Pairs of spin-labels were introduced by coupling to engineered cysteines on the protein surface, and the effects of labeling on ligand dissociation constants (Kd) and enzyme function were characterized. DEER results from three different mutants of CYP119 indicated that 4-Phenylimidazole binding results in a conformational state that is distinct substrate-free and Imidazole-bound forms. The DEER distance changes between the two conformational states were determined as 10A for two of the mutants and 12A for the other one. Data will also be presented for the complex between CYP119 its proposed substrate, lauric acid. These results will be discussed in terms of models for substrate recognition and gated functional behavior in these enzymes.

The role of conformational flexibility in β2‐microglobulin amyloid fibril formation at neutral pH

RATIONALE Amyloid formation is implicated in a number of human diseases. β2-microglobulin (β2m) is the precursor protein in dialysis-related amyloidosis and it has been shown that partial, or more complete, unfolding is key to amyloid fibril formation in this pathology. Here the relationship between conformational flexibility and β2m amyloid formation at physiological pH has been investigated.METHODS HDX-ESI-MS was used to study the conformational dynamics of β2m. Protein engineering, or the addition of Cu2+ ions, sodium dodecyl sulphate, trifluoroethanol, heparin, or protein stabilisers, was employed to perturb the conformational dynamics of β2m. The fibril-forming propensities of the protein variants and the wild-type protein in the presence of additives, which resulted in >5-fold increase in the EX1 rate of HDX, were investigated further.RESULTS ESI-MS revealed that HDX occurs via a mixed EX1/EX2 mechanism under all conditions. Urea denaturation and tryptophan fluorescence indicated that EX1 exchange occurred from a globally unfolded state in wild-type β2m. Although >30-fold increase in the HDX exchange rate was observed both for the protein variants and for the wild-type protein in the presence of specific additives, large increases in exchange rate did not necessarily result in extensive de novo fibril formation.CONCLUSIONS The conformational dynamics measured by the EX1 rate of HDX do not predict the ability of β2m to form amyloid fibrils de novo at neutral pH. This suggests that the formation of amyloid fibrils from β2m at neutral pH is dependent on the generation of one or more specific aggregation-competent species which facilitate self-assembly. Copyright © 2012 John Wiley & Sons, Ltd.

The role of conformational flexibility on protein supercharging in native electrospray ionization.

Effects of covalent intramolecular bonds, either native disulfide bridges or chemical crosslinks, on ESI supercharging of proteins from aqueous solutions were investigated. Chemically modifying cytochrome c with up to seven crosslinks or ubiquitin with up to two crosslinks did not affect the average or maximum charge states of these proteins in the absence of m-nitrobenzyl alcohol (m-NBA), but the extent of supercharging induced by m-NBA increased with decreasing numbers of crosslinks. For the model random coil polypeptide reduced/alkylated RNase A, a decrease in charging with increasing m-NBA concentration attributable to reduced surface tension of the ESI droplet was observed, whereas native RNase A electrosprayed from these same solutions exhibited enhanced charging. The inverse relationship between the extent of supercharging and the number of intramolecular crosslinks for folded proteins, as well as the absence of supercharging for proteins that are random coils in aqueous solution, indicate that conformational restrictions induced by the crosslinks reduce the extent of supercharging. These results provide additional evidence that protein and protein complex supercharging from aqueous solution is primarily due to partial or significant unfolding that occurs as a result of chemical and/or thermal denaturation induced by the supercharging reagent late in the ESI droplet lifetime.

Development of Spin-Labeled Pargyline Analogues as Specific Inhibitors of Human Monoamine Oxidases A and B

Three TEMPO-conjugated pargyline analogues (ParSL-1, ParSL-2, and ParSL-3) have been synthesized and their inhibitory properties tested for the two human monoamine oxidase isoforms (hMAOA and hMAOB). The three analogues differ in flexibility and substituent positions (para or meta) of the linkers connecting the TEMPO group to the pargyline phenyl ring. ParSL-1 contains a flexible acetamido (-CH(2)-CO-NH-) linker connecting the two moieties at the para position. In contrast, the TEMPO moieties in ParSL-2 and ParSL-3 are attached with rigid amido (-CO-NH-) linkers to the para or meta positions of the pargyline phenyl ring, respectively. These variations in conformational flexibility and substituent position are shown to have profound effects in tuning the specificities of these analogues toward the two MAO isoforms. ParSL-1 irreversibly inhibits either MAOA and MAOB, ParSL-2 inhibits only MAOB (K(i) = 15 +/- 5 microM), and ParSL-3 is found to be specific for MAOA (K(i) = 268 +/- 72 microM). These results thus provide additional insights into the role of conformational flexibility and structural properties of MAO inhibitors in tuning their isoform specificities. These active site probes have been used to determine the topological orientation of these enzymes in the mitochondrial membrane. Studies with intact mitochondria show MAOA is topologically on the cytosolic face of the outer membrane in human placenta but recombinant MAOA is situated on the opposite inner face in Pichia mitochondria. Recombinant MAOB is found to be situated on the cytosolic face of the outer membrane in Pichia mitochondria.

A buried lysine that titrates with a normal pKa: Role of conformational flexibility at the protein–water interface as a determinant of pKavalues

Previously we reported that Lys, Asp, and Glu residues at positions 66 and 92 in staphylococcal nuclease (SNase) titrate with pK(a) values shifted by up to 5 pK(a) units in the direction that promotes the neutral state. In contrast, the internal Lys-38 in SNase titrates with a normal pK(a). The crystal structure of the L38K variant shows that the side chain of Lys-38 is buried. The ionizable moiety is approximately 7 A from solvent and ion paired with Glu-122. This suggests that the pK(a) value of Lys-38 is normal because the energetic penalty for dehydration is offset by a favorable Coulomb interaction. However, the pK(a) of Lys-38 was also normal when Glu-122 was replaced with Gln or with Ala. Continuum electrostatics calculations were unable to reproduce the pK(a) of Lys-38 unless the protein was treated with an artificially high dielectric constant, consistent with structural reorganization being responsible for the normal pK(a) value of Lys-38. This reorganization must be local because circular dichroism and NMR spectroscopy indicate that the L38K protein is native-like under all conditions studied. In molecular dynamics simulations, the ion pair between Lys-38 and Glu-122 is unstable. The simulations show that a minor rearrangement of a loop is sufficient to allow penetration of water to the amino moiety of Lys-38. This illustrates both the important roles of local flexibility and water penetration as determinants of pK(a) values of ionizable groups buried near the protein-water interface, and the challenges faced by structure-based pK(a) calculations in reproducing these effects.

The role of conformational flexibility on the catalytic activity of norbornane-derived β-, γ- and δ-amino alcohols

Enantiopure norbornane-based γ-amino alcohols 1– 4 have been obtained from (+)-camphor and their catalytic behaviour as chiral ligands for the enantioselective addition of diethylzinc to benzaldehyde compared to these described for homologous β- and δ-amino alcohols. This has allowed the first study on the influence of the size of the catalytic zinc-chelate ring on the catalytic activity, which results in the unexpected observance of a non-linear correlation between enantioselectivity and chelate ring size (conformational flexibility). An empirical rationalisation of the observed phenomenon was realised on the basis of consideration of the energetically-favoured Noyori-type transition states.

The role of conformational flexibility on the association rate of protein complexes

The role of conformational flexibility on the association rate of protein complexes

The role of conformational flexibility in prion propagation and maintenance for Sup35p.

The [PSI(+)] factor of Saccharomyces cerevisiae is a protein-based genetic element (prion) comprised of a heritable altered conformation of the cytosolic translation termination factor Sup35p. In vitro, the prion-determining region (NM) of Sup35p undergoes conformational conversion from a highly flexible soluble state to structured amyloid fibers, with a rate that is greatly accelerated by preformed NM fiber nuclei. Nucleated conformational conversion is the molecular basis of the genetic inheritance of [PSI(+)] and provides a new model for studying amyloidogenesis. Here we investigate the importance of structure and structural flexibility in soluble NM. Elevated temperatures, chemical chaperones and certain mutations in NM increase or change its structural content and inhibit or enhance nucleated conformational conversion. We propose that the structural flexibility of NM is particularly suited to allowing heritable protein-based changes in cellular behavior.

Enzymatic methylation of L-isoaspartyl residues derived from aspartyl residues in affinity-purified calmodulin: The role of conformational flexibility in spontaneous isoaspartyl formation

We have investigated the formation of D-aspartyl and L-isoaspartyl (beta-aspartyl) residues and their subsequent methylation in bovine brain calmodulin by the type II protein carboxyl methyltransferase. Based on the results of studies with unstructured peptides and denatured proteins, it has been proposed that the major sites of carboxyl methylation in calmodulin are at L-isoaspartyl residues that originate from two Asn-Gly sequences. To test this hypothesis, we directly identified the sites of methylation in affinity-purified preparations of calmodulin by peptide mapping using the proteases trypsin, endoproteinase Lys-C, clostripain, chymotrypsin, and Staphylococcus aureus V8 protease. We found, however, that the major high-affinity sites of methylation originate from aspartyl residues at position 2 and at positions 78 and/or 80. The methylatable residue in the first case was shown to be L-isoaspartate by comparison of the properties of a synthetic peptide corresponding to the N-terminal 13 residues substituted with an L-iso-Asp residue at position 2. The second methylatable residue, probably derived from Asp78, also appears to be an L-isoaspartyl residue. These sites appear to be readily accessible to the methyltransferase and are present in relatively flexible regions of calmodulin that may allow the spontaneous degradation reactions to occur that generate L-isoaspartyl residues via succinimide intermediates. Interestingly, the four calcium binding regions, each containing 3-4 aspartyl and asparaginyl residues (including the two Asn-Gly sequences), do not appear to contribute to the high-affinity methyl acceptor sites, even when calcium is removed prior to the methylation reaction. We propose that methylatable residues do not form at these sites because of the inflexibility of these regions when calcium is bound.