Cyclodextrin inclusion compounds of vanadium complexes: Structural characterization and catalytic sulfoxidation

Reaction of potassium vanadate with the hydrazone ligand derived from Schiff-base condensation of salicylaldehyde and biphenyl-4-carboxylic acid hydrazide (H₂salhybiph) in the presence of two equivalents α-cyclodextrin (α-CD) in water yields the 1:2 inclusion compound K[VO₂(salhybiph)@(α-CD)₂]. Characterization in solution confirmed the integrity of the inclusion compound in the polar solvent water. The inclusion compound crystallizes together with additional water molecules as K[VO₂(salhybiph)@(α-CD)₂] · 18H₂O in the monoclinic space group P2(1). Two α-CD rings forming a hydrogen bonded head to head dimer are hosting the hydrophobic biphenyl side chain of the complex K[VO₂(salhybiph)]. The supramolecular aggregation of the inclusion compound in the solid state is established through hydrogen bonding interactions among adjacent α-CD hosts and with vanadate moieties of the guest complexes as well as ionic interactions with the potassium counterions. In contrast the supramolecular structure of the guest complex K[VO₂(salhybiph)] without the presence of CD host molecules is governed by π-π-stacking interactions and additional CH/π interactions. The new inclusion complex K[VO₂(salhybiph)@(α-CD)₂] and the analogous 1:1 inclusion compound with β-CD were tested as catalyst in the oxidation of methyl phenyl sulfide (thioanisol) using hydrogen peroxide as oxidant in a water/ethanol mixture, under neutral as well as acidic conditions.     

Crystal and molecular structure of V-anhydrous amylose

The conformation and crystalline packing of V-anhydrous amylose has been investigated by a combination of linked atom model building and X-ray diffraction analysis. The unit cell, the P2₁2₁2₁ space group, the left-handed sixfold helical conformation with all O(6) in gt rotational positions, and the intrahelical O(2)---O(3) and O(2)---O(6) hydrogen bonds are substantially in agreement with previous studies. A new model for packing of the chains in the unit cell and the presence of crystallographic water is proposed. Packing appears to be stabilized by corner-to-center chain O(2)---O(2) hydrogen bonds. The nature of the transition from the amylose–DMSO complex to V_a-amylose was considered and it is shown that the transition involves translation of the amylose chains parallel to the a and b unit cell axes with only slight changes in the orientation of the helix. No significant conformational changes result from the transition.     

Prediction of the native conformation of a polypeptide by a statistical-mechanical procedure. I. Backbone structure of enkephalin

A new methodology for theoretically predicting the native, three-dimensional structure of a polypeptide is presented. Based on equilibrium statistical mechanics, an algorithm has been designed to determine the probable conformation of a polypeptide by calculating conditional free-energy maps for each residue of the macromolecule. The conditional free-energy map of each residue is computed from a set of probability integrals, obtained by summing over the interaction energies of all pairs of nonbonded atoms of the whole molecule. By locating the region(s) of lowest free energy for each map, the probable conformation for each residue can be identified. The native structure of the polypeptide is assumed to be the combination of the probable conformations of the individual residues. All multidimensional probability integrals are evaluated by an adaptive Monte Carlo algorithm (SMAPPS —Statistical-Mechanical Algorithm for Predicting Protein Structure). The Monte Carlo algorithm searches the entire conformational space, adjusting itself automatically to concentrate its sampling in regions where the magnitude of the integrand is largest (“importance sampling”). No assumptions are made about the native conformation. The only prior knowledge necessary for the prediction of the native conformation is the amino acid sequence of the polypeptide. To test the effectiveness of the algorithm, SMAPPS was applied to the prediction of the native conformation of the backbone of Met-enkephalin, a pentapeptide. In the calculations, only the backbone dihedral angles (? and ψ) were allowed to vary; all side-chain (χ) and peptide-bond (ω) dihedral angles were kept fixed at the values corresponding to the alleged global minimum energy previously determined by direct energy minimization. For each conformation generated randomly by the Monte Carlo algorithm, the total conformational energy of the polypeptide was obtained from established empirical potential energy functions. Solvent effects were not included in the computations. With this initial application of SMAPPS , three distinct low-free-energy β-bend structures of Met-enkephalin were found. In particular, one of the structures has a conformation remarkably similar to the one associated with the previously alleged global minimum energy. The two additional structures of the pentapeptide have conformational energies lower than the previously computed low-energy structure. However, the Monte Carlo results are in agreement with an improved energy-minimization procedure. These initial results on the backbone structure of Met-enkephalin indicate that an equilibrium statistical-mechanical procedure, coupled with an adaptive Monte Carlo algorithm, can overcome many of the problems associated with the standard methods of direct energy minimization.     

Theoretical study on chiral recognition mechanism of methyl mandelate enantiomers on permethylated β-cyclodextrin

Host-guest interactions of permethylated β-cyclodextrin (PM-β-CD) with methyl mandelate enantiomers ((R/S)-MMA) were simulated using semiempirical PM3 and ONIOM (B3LYP/6-31G(d):PM3) method. The chiral recognition mechanism of (R/S)-MMA enantiomers on PM-β-CD was investigated. The binding energies for all orientations considered in this research are reported. The most stable geometry structures of the two complexes are different. The benzene ring of (R)-MMA locates horizontally approximately on the wider edge of the PM-β-CD cavity, but the aromatic ring of (S)-MMA is deeply included into the hydrophobic cavity. Furthermore, the results of NBO analysis show that the main driving forces in the inclusion process of PM-β-CD with (R/S)-MMA are hydrogen bonding interaction, dipole-dipole interaction, charge-transfer and hydrophobic interaction. The stabilization energy of the (R)-MMA/PM-β-CD complex is lower than that of the (S)-MMA/PM-β-CD complex. Moreover, the chiral carbon in MMA of (R/S)-MMA/PM-β-CD complexes are close to the C2 and C3 in the glucose unit. The chiral recognition mechanism is thus closely related to the chiral environment provided by C2 and C3 in the glucose unit and the degree of (R/S)-MMA and PM-β-CD inclusion.     

Formation of Inclusion Complexes of Cycldextrin with Ethanol under Anhydrous Conditions

Complex formation of poorly water soluble organic compounds with cyclodextrin (CD) is quite difficult in an aqueous cyclodextrin system. Formation of the inclusion complex of d-limonene, phenyl ethanol, acetophenone, or menthol was investigated in a slurry form of α-, β-, or γ-CD in organic solvents or alcohol under anhydrous conditions. Ethanol and methanol were found to be good solvents for this method. The use of ethanol as the solvent was investigated in greater detail. There existed an optimal amount of ethanol for the maximum inclusion of d-limonene as the guest compound. However, an excess of ethanol inhibited the inclusion. An adsorption model of alcohol on CD, analogous to the substrate inhibition model of enzyme kinetics, could correlate the inclusion ratio with the amount of alcohol added to CD.     

Substituent effects in the enantioselective reduction of acetophenones with nabh4 in the presence of β-cyclodextrin

The effect of substituent groups on asymmetric induction by β-cyclodextrin (β-CD) was investigated in the reduction of a series of o-, m-, and p-substituted acetophenones (X = H, Br, Cl, CH₃, NO₂, OCH₃) with aqueous NaBH₄. The inclusion of the ketones studied in β-CD led to water-insoluble compounds so that the reaction proceeded in the solid state. The substitutions resulted generally in higher enantioselectivities than that obtained for acetophenone indicating stronger host—guest interactions. Acetophenone and its m- and p-derivatives gave preponderantly the (?)-alcohol while the prevailing enantiomer was the (+)-alcohol in the case of the o-derivatives. The enantioface selectivity was found to be mainly governed by steric demands imposed by the size and the shape of the β-CD cavity in the case of the o-substituted acetophenones and by hydrophobic interactions in the case of the m-derivatives. A more complicated situation arose from the asymmetic reduction of p-derivatives where a combination of these factors with hydrogen bonding of the carbonyl group to the hydroxyls of β-CD are responsible for the enantioselectivity. © 1994 Wiley-Liss, Inc.     

Theoretical study on interactions of β-cyclodextrin with helicobacter pylori eradicating agent (TG44)

The inclusion complex of β-cyclodextrin (β-CD) and 4-methylbenzyl-4′-[trans-4- (guanidinomethyl)cylohexylcarbonyloxy]-biphenyl-4-carboxlylate monohydrochloride (TG44) had been investigated by using densify functional theory (DFT) and PM3 semiempirical method. The results indicate that the β-CD includes predominantly the biphenyl moiety of TG44, and the inclusion complex formed by TG44 entering into the cavity of β-CD from its narrow side (the primary hydroxyl group side) is more stable than that formed by TG44 entering into the cavity of β-CD from its wide side (the secondary hydroxyl group side). The negative enthalpy changes calculated from the statistical thermodynamic calculations at 1 atm and 298.15 K suggest that the inclusion complexes are favored enthalpy-driven processes. The molecular modeling results are in good agreement with the experiment for 2D ¹H–¹³C H HETCOR spectroscopic and H-NMR spectroscopic observations.     

Effect of O(2′)-methylation on the stability of polynucleotide helices

The effect of ribose(O2′)-methylation on the stability of (O2′)-methylated polyribonucleotide helices has been studied by conformational energy calculations. The preferred orientation of the methyl group is found to further stabilize the helical phosphodiester conformation (g^?,g^?) due to the enhanced short-range interactions arising between the methyl groups and the adjacent ribose moieties. The experimentally observed increase in melting temperature of (O2′)-alkylated polyribonucleotides is thus attributable to the enhanced stability of the helical backbone conformation.     

Equilibrium folding and unfolding pathways for a model protein

The folding–unfolding process of reduced bovine pancreatic trypsin inhibitor was investigated with an idealized model employing approximate free energies. The protein is regarded to consist of only C^α and C^β atoms. The backbone dihedral angles are the only conformational variables and are permitted to take discrete values at every 10°. Intraresidue energies consist of two terms: an empirical part taken from the observed frequency distributions of (?,ψ) and an additional favorable energy assigned to the native conformation of each residue. Interresidue interactions are simplified by assuming that there is an attractive energy operative only between residue pairs in close contact in the native structure. A total of 230,000 molecular conformations, with no atomic overlaps, ranging from the native state to the denatured state, are randomly generated by changing the sampling bias. Each conformation is classified according to its conformational energy, F; a conformational entropy, S(F) is estimated for each value of F from the number of samples. The dependence of S(F) on energy reveals that the folding–unfolding transition for this idealized model is an “all-or-none” type; this is attributable to the specific long-range interactions. Interresidue contact probabilities, averaged over samples representing various stages of folding, serve to characterize folding intermediates. Most probable equilibrium pathways for the folding–unfolding transition are constructed by connecting conformationally similar intermediates. The specific details obtained for bovine pancreatic trypsin inhibitor are as follows: (1) Folding begins with the appearance of nativelike medium-range contacts at a β-turn and at the α-helix. (2) These grow to include the native pair of interacting β-strands. This state includes intact regular secondary conformations, as well as the interstrand sheet contacts, and corresponds to an activated state with the highest free energy on the pathway. (3) Additional native long-range contacts are completely formed either toward the amino terminus or toward the carboxyl terminus. (4) In a final step, the missing contacts appear. Although these folding pathways for this model are not consistent with experimental reports, it does indicate multiple folding pathways. The method is general and can be applied to any set of calculated conformational energies and furthermore permits investigation of gross folding features.     

Optical characteristics of carboxyl group in relation to the circular dichroic properties and dissociation constants of glycosaminoglycans

Circular dichroism studies of glycosaminoglycan including chemically transformed heparins at various pH values reveal that carboxyl chromophore plays an important role in the dichroic behavior of the polymers. With decreasing pH, iduronic acid-containing glycosaminoglycans show increased negative ellipticity near 220 nm whereas the polymers containing glucuronic acid display enhanced negative dichroism near 230 nm and decreased negative dichroism around 210 nm. The pH-dependent optical properties have been utilized to determine the pK_a values of uronic acid moieties. The acid strengths of the iduronic acid-containing glycosaminoglycans are inherently smaller than those of corresponding glucuronic acid-containing polymers. Glycosaminoglycans in which the amino sugars are linked with iduronic acid display a very weak n → π^* amide transition, or none. The rotational strength at 210 nm of these polymers is largely due to iduronic acid moieties. The CD variations above 200 nm with change in pH do not indicate any major conformational transition of the molecules but the difference between dermatan sulfate and heparin can be attributed to difference either in iduronic acid conformation or in intersaccharide linkages.     

Understanding the roles of amino acid residues in tertiary structure formation of chignolin by using molecular dynamics simulation

Chignolin is a 10-residue peptide (GYDPETGTWG) that forms a stable beta-hairpin structure in water. However, its design template, GPM12 (GYDDATKTFG), does not have a specific structure. To clarify which amino acids give it the ability to form the beta-hairpin structure, we calculated the folding free-energy landscapes of chignolin, GPM12, and their chimeric peptides using multicanonical molecular dynamics (MD) simulation. Cluster analysis of the conformational ensembles revealed that the native structure of chignolin was the lowest in terms of free energy while shallow local minima were widely distributed in the free energy landscape of GPM12, in agreement with experimental observations. Among the chimeric peptides, GPM12(D4P/K7G) stably formed the same beta-hairpin structure as that of chignolin in the MD simulation. This was confirmed by nuclear magnetic resonance (NMR) spectroscopy. A comparison of the free-energy landscapes showed that the conformational distribution of the Asp3-Pro4 sequence was inherently biased in a way that is advantageous both to forming hydrogen bonds with another beta-strand and to initiating loop structure. In addition, Gly7 helps stabilize the loop structure by having a left-handed alpha-helical conformation. Such a conformation is necessary to complete the loop structure, although it is not preferred by other amino acids. Our results suggest that the consistency between the short-range interactions that determine the local geometries and the long-range interactions that determine the global structure is important for stable tertiary structure formation.     

Probing the Transition State of the Allosteric Pathway of the Shaker Kv Channel Pore by Linear Free-Energy Relations

Long-range coupling between distant functional elements of proteins may rely on allosteric communication trajectories lying along the protein structure, as described in the case of the Shaker voltage-activated potassium (Kv) channel model allosteric system. Communication between the distant Kv channel activation and slow inactivation pore gates was suggested to be mediated by a network of local pairwise and higher-order interactions among the functionally unique residues that constitute the allosteric trajectory. The mechanism by which conformational changes propagate along the Kv channel allosteric trajectory to achieve pore opening, however, remains unclear. Such conformational changes may propagate in either a concerted or a sequential manner during the reaction coordinate of channel opening. Residue-level structural information on the transition state of channel gating is required to discriminate between these possibilities. Here, we combine patch-clamp electrophysiology recordings of Kv channel gating and analysis using linear free-energy relations, focusing on a select set of residues spanning the allosteric trajectory of the Kv channel pore. We show that all allosteric trajectory residues tested exhibit an open-like conformation in the transition state of channel opening, implying that coupling interactions occur along the trajectory break in a concerted manner upon moving from the closed to the open state. Energetic coupling between the Kv channel gates thus occurs in a concerted fashion in both the spatial and the temporal dimensions, strengthening the notion that such trajectories correspond to pathways of mechanical deformation along which conformational changes propagate.     

Speed of Conformational Change: Comparing Explicit and Implicit Solvent Molecular Dynamics Simulations

Adequate sampling of conformation space remains challenging in atomistic simulations, especially if the solvent is treated explicitly. Implicit-solvent simulations can speed up conformational sampling significantly. We compare the speed of conformational sampling between two commonly used methods of each class: the explicit-solvent particle mesh Ewald (PME) with TIP3P water model and a popular generalized Born (GB) implicit-solvent model, as implemented in the AMBER package. We systematically investigate small (dihedral angle flips in a protein), large (nucleosome tail collapse and DNA unwrapping), and mixed (folding of a miniprotein) conformational changes, with nominal simulation times ranging from nanoseconds to microseconds depending on system size. The speedups in conformational sampling for GB relative to PME simulations, are highly system- and problem-dependent. Where the simulation temperatures for PME and GB are the same, the corresponding speedups are approximately onefold (small conformational changes), between ∼1- and ∼100-fold (large changes), and approximately sevenfold (mixed case). The effects of temperature on speedup and free-energy landscapes, which may differ substantially between the solvent models, are discussed in detail for the case of miniprotein folding. In addition to speeding up conformational sampling, due to algorithmic differences, the implicit solvent model can be computationally faster for small systems or slower for large systems, depending on the number of solute and solvent atoms. For the conformational changes considered here, the combined speedups are approximately twofold, ∼1- to 60-fold, and ∼50-fold, respectively, in the low solvent viscosity regime afforded by the implicit solvent. For all the systems studied, 1) conformational sampling speedup increases as Langevin collision frequency (effective viscosity) decreases; and 2) conformational sampling speedup is mainly due to reduction in solvent viscosity rather than possible differences in free-energy landscapes between the solvent models.     

Kinetic pathways of beta-hairpin (un)folding in explicit solvent

We examine the dynamical (un)folding pathways of the C-terminal beta-hairpin of protein G-B1 at room temperature in explicit solvent, by employing transition path sampling algorithms. The path ensembles contain information on the folding kinetics, including solvent motion. We determine the transition state ensembles for the two main transitions: 1), the hydrophobic collapse; and 2), the backbone hydrogen bond formation. In both cases the transition state ensembles are characterized by a layer (1) or a strip (2) of water molecules in between the two hairpin strands, supporting the hypothesis of the solvent as lubricant in the folding process. The transition state ensembles do not correspond with saddle points in the equilibrium free-energy landscapes. The kinetic pathways are thus not completely determined by the free-energy landscape. This phenomenon can occur if the order parameters obey different timescales. Using the transition interface sampling technique, we calculate the rate constants for (un)folding and find them in reasonable agreement with experiments, thus supporting the validation of using all-atom force fields to study protein folding.     

Sequence-dependence of secondary structure formation: conformational studies of host-guest peptides in alpha-helix and beta-structure supporting media

A newly designed host–guest approach is introduced as a experimental tool to explore the relationship between the sequence of peptides and their secondary structure. From the CD spectra of the host–guest peptides studied, a tentative scale for the α-helix potential in 2,2,2-trifluorethanol of guest amino acids is delineated. The conformational preferences are also examined in β-structure supporting media (solid state, CH₂Cl₂, CH₃OH, H₂O) using ir-absorption and CD techniques. Scales for the β-forming tendency of guest amino acid residues in the different media are delineated. It is shown that the preferred conformation of the host–guest peptides is a function of the medium, the chain length, and the protecting groups. Given the fact that conformational effects are important in peptide synthesis, the tentative scales may serve as a guideline to predict secondary structures of side-chain-protected or -deprotected peptides in a given solvent, complementing the well-known empirical conformational prediction parameters.     

Flexible Gates Generate Occluded Intermediates in the Transport Cycle of LacY

The major facilitator superfamily (MFS) transporter lactose permease (LacY) alternates between cytoplasmic and periplasmic open conformations to co-transport a sugar molecule together with a proton across the plasma membrane. Indirect experimental evidence suggested the existence of an occluded transition intermediate of LacY, which would prevent leaking of the proton gradient. As no experimental structure is known, the conformational transition is not fully understood in atomic detail. We simulated transition events from a cytoplasmic open conformation to a periplasmic open conformation with the dynamic importance sampling molecular dynamics method and observed occluded intermediates. Analysis of water permeation pathways and the electrostatic free-energy landscape of a solvated proton indicated that the occluded state contains a solvated central cavity inaccessible from either side of the membrane. We propose a pair of geometric order parameters that capture the state of the pathway through the MFS transporters as shown by a survey of available crystal structures and models. We present a model for the occluded state of apo-LacY, which is similar to the occluded crystal structures of the MFS transporters EmrD, PepT_So, NarU, PiPT and XylE. Our simulations are consistent with experimental double electron spin–spin distance measurements that have been interpreted to show occluded conformations. During the simulations, a salt bridge that has been postulated to be involved in driving the conformational transition formed. Our results argue against a simple rigid-body domain motion as implied by a strict “rocker-switch mechanism” and instead hint at an intricate coupling between two flexible gates.     

Cloning and Sequencing of the xynC Gene Encoding Acid Xylanase of Aspergillus kawachii

The molecular conformation of elsinan, consisting of (1 → 3)-α-linked maltotriose and α-maltotetraose units, was studied by X-ray diffraction coupled with conformational analysis. The quality of the X-ray fiber pattern obtained from elsinan was very poor, but the layer line spacing (45 Å), the probable presence of (005) reflection and a similar pattern with the powder pattern of a low molecular weight poly[(1 →3)-α-maltotriose] segment (DP about 35) suggested that the poly[(1 →3)-linked-α-maltotriose] segment (MTR part) of elsinan chain took a five-fold helical structure with an asymmetric unit of maltotriose. Conformational analysis for the five-fold helix of the MTR part pointed out that two left handed helices, - 5/1 and - 5/2, were energetically probable.     

A Catalytically Disabled Double Mutant of Src Tyrosine Kinase Can Be Stabilized into an Active-Like Conformation

Tyrosine kinases are enzymes playing a critical role in cellular signaling. Molecular dynamics umbrella sampling potential of mean force computations are used to quantify the impact of activating and inactivating mutations of c-Src kinase. The potential of mean force computations predict that a specific double mutant can stabilize c-Src kinase into an active-like conformation while disabling the binding of ATP in the catalytic active site. The active-like conformational equilibrium of this catalytically dead kinase is affected by a hydrophobic unit that connects to the hydrophobic spine network via the C-helix. The αC-helix plays a crucial role in integrating the hydrophobic residues, making it a hub for allosteric regulation of kinase activity and the active conformation. The computational free-energy landscapes reported here illustrate novel design principles focusing on the important role of the hydrophobic spines. The relative stability of the spines could be exploited in future efforts to artificially engineer active-like but catalytically dead forms of protein kinases.     

Metal Ion Binding and Conformational Transitions in Concanavalin A: A Structure-Function Study

Abstract

The affinity of the lectin Concanavalin A (Con A) for saccharides, and its requirement for metal ions such as Mn²⁺ and Ca²⁺, have been known for about 50 years. However the relationship between metal ion binding and the saccharide binding activity of Con A has only recently been examined in detail. Brown et al. (Biochemistry 16, 3883 (1977)) showed that Con A exists as a mixture of two conformational states: a “locked” form and an “unlocked” form. The unlocked form of the protein weakly binds metal ions and saccharide, and is the predominate conformation of demetallized Con A (apo-Con A) at equilibrium. The locked form binds two metal ions per monomer with the resulting complex(es) possessing full saccharide binding activity. Brown and coworkers measured the kinetics of the transition of the unlocked form to the fully metallized locked conformation containing Mn²⁺and Ca²⁺. They also demonstrated that Mn²⁺ alone could form a locked ternary complex with Con A, and that rapid removal of the ions resulted in a metastable form of apo-Con A in the locked conformation which slowly (hours at 25°C) reverted back to (predominantly) the unlocked conformation. The ability to form either conformation in the absence or presence of metal ions has thus allowed us to explore the relationship between metal ion binding and conformational transitions in Con A as determinants of the saccharide binding activity of the lectin.

Based on the kinetics of the transition of unlocked apo-Con A to fully metallized locked Con A, and X-ray crystallographic data, it appears that the transition between the two conformations of Con A involves a cis-trans isomerization of an Ala-Asp peptide bond in the backbone of the protein, near one of the two metal ion binding sites. The relatively large activation energy for the transition (～ 22 kcal M^?1) results in relatively slow interconversions between the conformations (from minutes to days), whereas the equilibria with metal ions and saccharide are rapid. Thus, many metastable complexes can be formed and a variety of transition pathways between the two conformations studied.

We have identified and characterized binary, ternary, and quaternary complexes of both conformations of Con A containing Mn²⁺ and saccharide, and have determined both metalion and saccharide dissociation constants for all of them, as well as equilibrium and kinetic values for the conformational transitions between them. The main finding is that saccharide binds very weakly (K_d～2 M) to unlocked apo-Con A and very tightly to the locked ternary Mn²⁺-Con A complex (K_d～ 10^?4 M). Saccharide binding increases along the various pathways connecting these two species in a nonadditive fashion. Thus, both conformation and metal ion binding determine the saccharide affinity of each complex, although the specificity of saccharide binding of the various species is maintained throughout.     

CD44 Receptor Unfolding Enhances Binding by Freeing Basic Amino Acids to Contact Carbohydrate Ligand

The extracellular carbohydrate-binding domain of the Type I transmembrane receptor CD44 is known to undergo affinity switching, where change in conformation leads to enhanced binding of its carbohydrate ligand hyaluronan. Separate x-ray crystallographic and NMR experiments have led to competing explanations, with the former supporting minor conformational changes at the binding site and the latter a major order-to-disorder unfolding transition distant from the binding site. Here, all-atom explicit-solvent molecular dynamics studies employing adaptive biasing force sampling revealed a substantial favorable free-energy change associated with contact formation between the Arg⁴¹ side chain and hyaluronan at the binding site, independent of whether the distant site was ordered or disordered. Analogous computational experiments on Arg⁴¹Ala mutants showed loss of this favorable free-energy change, consistent with existing experimental data. More provocatively, the simulation data revealed the molecular mechanism by which the order-to-disorder transition enhances hyaluronan binding: in the disordered state, a number of basic residues gain sufficient conformational freedom—lacking in the ordered state—to spontaneously form side-chain contacts with hyaluronan. Mutation of these residues to Ala had been known to decrease binding affinity, but there had previously been no structural explanation, given their lack of proximity to the carbohydrate-binding site in existing structures of the complex.