Long-range Hydrophobic Interactions Research Articles

Effect of an electric field on dewetting transition of nitrogen-water system

We investigate the influence of an external electric field on the dewetting behavior of nitrogen-water systems between two hydrophobic plates using molecular dynamics simulations. It is found that the critical distance of dewetting increases obviously with the electric field strength, indicating that the effective range of hydrophobic attraction is extended. The mechanism behind this interesting phenomenon is related to the rearrangement of hydrogen bond networks between water molecules induced by the external electric field. Changes in the hydrogen bond networks and in the dipole orientation of the water molecules result in the redistribution of the neutral nitrogen molecules, especially in the region close to the hydrophobic plates. Our findings may be helpful for understanding the effects of the electric field on the long-range hydrophobic interactions.

Biofouling-Inspired Growth of Superhydrophilic Coating of Polyacrylic Acid on Hydrophobic Surfaces for Excellent Anti-Fouling.

In this work, we demonstrated effective adsorption of poly(acrylic acid) (PAA) in saline water on various hydrophobic substrates, ranging from polyethylene and polytetrafluoroethylene, to form densely packed monolayers with water contact angle as low as 6.5° in air. This was a result of the synergy of long-range hydrophobic interactions between individual PAA chains and hydrophobic surfaces and short-range hydrogen bonding between neighboring PAA chains, reminiscent of the interaction balance encountered in biofouling. The PAA monolayers adsorbed on hydrophobic surfaces showed the ultrahigh packing density of surface COOH groups of 4.8 nm-2, which contributed to the surface superhydrophilicity and its stability against surface reconstruction during aging even at temperature higher than PAA glass transition. Further, conjugation of the adsorbed PAA monolayers with polyethylene glycol results in excellent antifouling with nearly zero adsorption of proteins.

Defect-rich porous carbon with anti-interference capability for adsorption of bisphenol A via long-range hydrophobic interaction synergized with short-range dispersion force

Wastewater features-directed design of an adsorbent is promising but challenging strategy for sustainable remediation of actual bisphenol A (BPA)-polluted water. Herein, we report that the discarded cigarette butt-derived porous carbon (AC-800) exhibit high capacity (865 mg/g), rapid reaction rate (186.9 mg/g/min) and outstanding durability for adsorption of BPA. Different from the most reported carbon-based adsorbents, quantitative structure-activity relationship studies unveil that graphitic defect plays a crucial role in the improvement of adsorptivity. Further studies illuminate that π-π interactions, electrostatic attraction and hydrogen-bond interaction play a negligible role whereas long-range hydrophobic interaction synergized with short-range dispersion force make a substantial contribution to BPA adsorption on AC-800. Benefited from this unique adsorption mechanism, AC-800 features a remarkable anti-interference capability and realizes the efficient clean-up of BPA from actual wastewater with complex backgrounds. This work sheds new light on mechanistic insight into the BPA adsorption on carbon-based materials and develops a fit-for-purpose designed adsorbent toward green remediation of practical wastewater.

Identification of an α-MoRF in the Intrinsically Disordered Region of the Escargot Transcription Factor.

Molecular recognition features (MoRFs) are common in intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs). MoRFs are in constant order–disorder structural transitions and adopt well-defined structures once they are bound to their targets. Here, we study Escargot (Esg), a transcription factor in Drosophila melanogaster that regulates multiple cellular functions, and consists of a disordered N-terminal domain and a group of zinc fingers at its C-terminal domain. We analyzed the N-terminal domain of Esg with disorder predictors and identified a region of 45 amino acids with high probability to form ordered structures, which we named S2. Through 54 μs of molecular dynamics (MD) simulations using CHARMM36 and implicit solvent (generalized Born/surface area (GBSA)), we characterized the conformational landscape of S2 and found an α-MoRF of ∼16 amino acids stabilized by key contacts within the helix. To test the importance of these contacts in the stability of the α-MoRF, we evaluated the effect of point mutations that would impair these interactions, running 24 μs of MD for each mutation. The mutations had mild effects on the MoRF, and in some cases, led to gain of residual structure through long-range contacts of the α-MoRF and the rest of the S2 region. As this could be an effect of the force field and solvent model we used, we benchmarked our simulation protocol by carrying out 32 μs of MD for the (AAQAA)3 peptide. The results of the benchmark indicate that the global amount of helix in shorter peptides like (AAQAA)3 is reasonably predicted. Careful analysis of the runs of S2 and its mutants suggests that the mutation to hydrophobic residues may have nucleated long-range hydrophobic and aromatic interactions that stabilize the MoRF. Finally, we have identified a set of residues that stabilize an α-MoRF in a region still without functional annotations in Esg.

Computational investigation on the effect of Oleuropein aglycone on the α-synuclein aggregation

Parkinson’s disease (PD) is considered to be the second most common progressive neurodegenerative brain disorder after Alzheimer’s disease, which is caused by misfolding and aggregation of Alpha-synuclein (α-synuclein). It is characterized by distinct aggregated fibrillary form of α-synuclein known as the Lewy bodies and Lewy neurites. The most promising approach to combat PD is to prevent the misfolding and subsequent aggregation of α-synuclein. Recently, Oleuropein aglycone (OleA) has been reported to stabilize the monomeric structure of α-synuclein, subsequently favoring the growth of nontoxic aggregates. Therefore, understanding the conformational dynamics of α-synuclein monomer in the presence of OleA is significant. Here, we have investigated the effect of OleA on the conformational dynamics and the aggregation propensity of α-synuclein using molecular dynamics simulation. From molecular dynamics trajectory analysis, we noticed that when OleA is bound to α-synuclein, the intramolecular distance between non-amyloid-β component domain and C-terminal domain of α-synuclein was increased, whereas long-range hydrophobic interactions between the two region were reduced. Oleuropein aglycone was found to interact with the N-terminal domain of α-synuclein, making this region unavailable for interaction with membranes and lipids for the formation of cellular toxic aggregates. From the binding-free energy analysis, we found binding affinity between α-synuclein and OleA to be indeed high (ΔG bind = –12.56 kcal mol−1 from MM-PBSA and ΔG bind = –27.41 kcal mol−1from MM-GBSA). Our findings in this study thus substantiate the effect of OleA on the structure and stabilization of α-synuclein monomer that subsequently favors the growth of stable and nontoxic aggregates. Communicated by Ramaswamy H. Sarma

Disassociation of β1-α1-β2 from the α2-α3 domain of prion protein (PrP) is a prerequisite for the conformational conversion of PrPC into PrPSc: Driven by the free energy landscape

Misfolding of the cellular prion protein (PrPC) into β-sheet-rich scrapie form (PrPSc) is associated with transmissible spongiform encephalopathies. A point mutation F198S is responsible for the development of a rare inherited Gerstmann-Straussler-Scheinker disease caused by the aggregation of PrPC. Thus, identification and the structural characterization of aggregation-prone regions are essential to delineate the conversion of PrPC to the disease-associated PrPSc upon F198S mutation. In the present study, molecular dynamics simulations on the wild-type PrP (WT-PrP) and its mutant were performed to explore the structural basis responsible for aggregation driven by the mutation. Secondary structure analysis revealed that the mutant exhibited a partial unfolding on α2 and the complete distortion in the 310-helix of the β2-α2 loop. Remarkably, the β2-α2 loop is in proximity to α3 attributed by the long-range hydrophobic interactions and such structural intimacy is not observed in the WT-PrP. Owing to this, the β1-α1-β2 regions have separated from α2-α3 domain resulting in the impairment on the hydrogen bond between α1 and α3. Thus, the present study provides a detailed structural description of the F198S mutant in line with previous experimental results and delivers insights into the structural basis responsible for the conversion of PrPC to the disease-associated PrPSc.

Cryo-EM structures of Helicobacter pylori vacuolating cytotoxin A oligomeric assemblies at near-atomic resolution

Human gastric pathogen Helicobacter pylori (H. pylori) is the primary risk factor for gastric cancer and is one of the most prevalent carcinogenic infectious agents. Vacuolating cytotoxin A (VacA) is a key virulence factor secreted by H. pylori and induces multiple cellular responses. Although structural and functional studies of VacA have been extensively performed, the high-resolution structure of a full-length VacA protomer and the molecular basis of its oligomerization are still unknown. Here, we use cryoelectron microscopy to resolve 10 structures of VacA assemblies, including monolayer (hexamer and heptamer) and bilayer (dodecamer, tridecamer, and tetradecamer) oligomers. The models of the 88-kDa full-length VacA protomer derived from the near-atomic resolution maps are highly conserved among different oligomers and show a continuous right-handed β-helix made up of two domains with extensive domain-domain interactions. The specific interactions between adjacent protomers in the same layer stabilizing the oligomers are well resolved. For double-layer oligomers, we found short- and/or long-range hydrophobic interactions between protomers across the two layers. Our structures and other previous observations lead to a mechanistic model wherein VacA hexamer would correspond to the prepore-forming state, and the N-terminal region of VacA responsible for the membrane insertion would undergo a large conformational change to bring the hydrophobic transmembrane region to the center of the oligomer for the membrane channel formation.

A Small Molecule Causes a Population Shift in the Conformational Landscape of an Intrinsically Disordered Protein.

Intrinsically disordered proteins (IDPs) have roles in myriad biological processes and numerous human diseases. However, kinetic and amplitude information regarding their ground-state conformational fluctuations has remained elusive. We demonstrate using nuclear magnetic resonance (NMR)-based relaxation dispersion that the D2 domain of p27Kip1, a prototypical IDP, samples multiple discrete, rapidly exchanging conformational states. By combining NMR with mutagenesis and small-angle X-ray scattering (SAXS), we show that these states involve aromatic residue clustering through long-range hydrophobic interactions. Theoretical studies have proposed that small molecules bind promiscuously to IDPs, causing expansion of their conformational landscapes. However, on the basis of previous NMR-based screening results, we show here that compound binding only shifts the populations of states that existed within the ground state of apo p27-D2 without changing the barriers between states. Our results provide atomic resolution insight into how a small molecule binds an IDP and emphasize the need to examine motions on the low microsecond time scale when probing these types of interactions.

Modulation of the Intrinsic Helix Propensity of an Intrinsically Disordered Protein Reveals Long-Range Helix–Helix Interactions

Intrinsically disordered proteins (IDPs) are widespread and important in biology but defy the classical protein structure-function paradigm by being functional in the absence of a stable, folded conformation. Here we investigate the coupling between transient secondary and tertiary structure in the protein activator for thyroid hormone and retinoid receptors (ACTR) by rationally modulating the helical propensity of a partially formed α-helix via mutations. Eight mutations predicted to affect the population of a transient helix were produced and investigated by NMR spectroscopy. Chemical shift changes distant to the mutation site are observed in regions containing other transient helices indicating that distant helices are stabilized through long-range hydrophobic helix-helix interactions and demonstrating the coupling of transient secondary and tertiary structure. The long-range structure of ACTR is also probed using paramagnetic relaxation enhancements (PRE) and residual dipolar couplings, which reveal an additional long-range contact between the N- and C-terminal segments. Compared to residual dipolar couplings and PRE, modulation of the helical propensity by mutagenesis thus reveals a different set of long-range interactions that may be obscured by stronger interactions that dominate other NMR measurements. This approach thus offers a complementary and generally applicable strategy for probing long-range structure in disordered proteins.

Self-organized criticality in proteins: Hydropathic roughening profiles of G-protein-coupled receptors

Proteins appear to be the most dramatic natural example of self-organized criticality (SOC), a concept that explains many otherwise apparently unlikely phenomena. Protein conformational functionality is often dominated by long-range hydrophobic or hydrophilic interactions which both drive protein compaction and mediate protein-protein interactions. Superfamily transmembrane G-protein-coupled receptors (GPCRs) are the largest family of proteins in the human genome; their amino acid sequences form the largest database for protein-membrane interactions. While there are now structural data on the heptad transmembrane structures of representatives of several heptad families, here we show how fresh insights into global and some local chemical trends in GPCR properties can be obtained accurately from sequences alone, especially by algebraically separating the extracellular and cytoplasmic loops from transmembrane segments. The global mediation of long-range water-protein interactions occurs in conjunction with modulation of these interactions by roughened interfaces. Hydropathic roughening profiles are defined here solely in terms of amino acid sequences, and knowledge of protein coordinates is not required. Roughening profiles both for GPCR and some simpler protein families display accurate and transparent connections to protein functionality, and identify natural length scales for protein functionality.

Robustness in Protein Folding Revealed by Thermodynamics Calculations

Long-range intraprotein interactions play important roles in protein folding. In the present study, we use two variants of the B domain of protein A (BdpA F14W/G30A and BdpA_ds) and two variants of the Trp cage (TC5b_P1 and TC5b_P2) as models to investigate how long-range hydrophobic interactions affect protein tertiary and secondary structures. The mutation of the selected residues (BdpA F14W/G30A) or the change in the sequence order of Helix1 and Helix2 (BdpA_ds) changes detailed hydrophobic interactions. However, this change does not alter the global three-helix-bundle structure of BdpA and the overall shape of the folding free-energy landscape. It does affect the formation and stability of individual secondary structures. Similarly, the addition of an extra segment to the C-terminus of Trp-cage increases the number of long-range hydrophobic interactions without making any significant change of the native structure of Trp-cage. These results show the robustness of the overall protein folding, where rather large sequence changes exert significant influences on secondary but not tertiary structures.

Conformational Dynamics of the Trp-Cage Miniprotein at Its Folding Temperature

The folding temperature of the trp-cage mini-protein was determined to be in the range 311-317 K depending on the method used. Our study is focused on determining the structure and dynamics of the polypeptide chain close to its unfolding or melting temperature. At T = 305 K, Trp6-Arg16 and Trp6-Pro12 long-range interactions are observed, and at T = 313 K, only the Trp6-Arg16 interactions remain, while all of mentioned interactions are observed in the native state of the protein. Partial (at T = 305 K) and complete (at T = 313 K) melting of the N-terminal α-helix is observed, manifested by the appearance of minor sets of signals in NMR spectra. Our key findings are: (i) conformational phase transition (melting point) could be described as a cooperative breaking of the Trp6-Pro12 long-range hydrophobic interaction and the melting of the N-terminal α-helix; (ii) many ROE signals corresponding to local or short-range interactions vanish rapidly with temperature increase; however, long-range interaction such as Trp6-Arg16 remains until 313 K. The presence of the native long-range interaction at 313 K makes that conformational ensemble resemble a very diffuse native state structure, but it is not a simple mixture of the folded and unfolded states, as could be expected on the basis of the common two-state folding mechanism.

Hydrophobic interactions between polymer surfaces: using polystyrene as a model system

The hydrophobic interaction plays a critical role in a wide range of molecular phenomena in numerous biological and engineering systems. Using a Surface Forces Apparatus (SFA) coupled with a top-view optical microscope, we have directly measured and visualized the interactions between two polystyrene surfaces in different electrolyte solutions (i.e., NaCl, CaCl2, HCl and CH3COOH). It is evident that the long-range hydrophobic interaction measured is due to bridging of microscopic and sub-microscopic bubbles on polystyrene surfaces. The range of the hydrophobic interaction decreases with increasing the electrolyte concentration for NaCl and CaCl2, but shows no significant change for HCl and CH3COOH, which is related to the formation and stability of bubbles on hydrophobic surfaces due to the ion specificity. The range of the hydrophobic interactions was reduced to about 10–20 nm by degassing the aqueous solutions, but gradually recovered when re-exposing the degassed solution to air. Our results indicate that dissolved gasses in solutions play a crucial role in the hydrophobic interactions of polymer surfaces, and support a three-regime hydrophobic interaction model proposed. More interesting, spontaneous cavitation of water between two interacting polystyrene surfaces was directly observed in degassed aqueous solution at a separation of ≤20 nm. The interfacial energy of polystyrene in various aqueous solutions was determined to be γ = 42 ± 5 mJ m−2, close to the values measured in air. Interesting fracture patterns were also observed associated with the separation of two hydrophobic polymer surfaces in aqueous solutions, but not in air, indicating that hydrophobic force plays an important role in adhesion-induced fracture of polymer surfaces and thin films. Our study provides new insight into the basic hydrophobic interaction mechanism of polymers and biomacromolecules.

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin‐binding protein G from Streptococcus. IV. Implication for the mechanism of folding of the parent protein

A 34-residue alpha/beta peptide [IG(28-61)], derived from the C-terminal part of the B3 domain of the immunoglobulin binding protein G from Streptoccocus, was studied using CD and NMR spectroscopy at various temperatures and by differential scanning calorimetry. It was found that the C-terminal part (a 16-residue-long fragment) of this peptide, which corresponds to the sequence of the beta-hairpin in the native structure, forms structure similar to the beta-hairpin only at T = 313 K, and the structure is stabilized by non-native long-range hydrophobic interactions (Val47-Val59). On the other hand, the N-terminal part of IG(28-61), which corresponds to the middle alpha-helix in the native structure, is unstructured at low temperature (283 K) and forms an alpha-helix-like structure at 305 K, and only one helical turn is observed at 313 K. At all temperatures at which NMR experiments were performed (283, 305, and 313 K), we do not observe any long-range connectivities which would have supported packing between the C-terminal (beta-hairpin) and the N-terminal (alpha-helix) parts of the sequence. Such interactions are absent, in contrast to the folding pathway of the B domain of protein G, proposed recently by Kmiecik and Kolinski (Biophys J 2008, 94, 726-736), based on Monte-Carlo dynamics studies. Alternative folding mechanisms are proposed and discussed.

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long‐range hydrophobic interactions

A 20-residue peptide, IG(42-61), derived from the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptoccocus was studied using circular dichroism, nuclear magnetic resonance (NMR) spectroscopy at various temperatures and by differential scanning calorimetry (DSC). Unlike other related peptides studied so far, this peptide displays two heat capacity peaks in DSC measurements (at a scanning rate of 1.5 deg/min at a peptide concentration of 0.07 mM), which suggests a three-state folding/unfolding process. The results from DSC and NMR measurements suggest the formation of a dynamic network of hydrophobic interactions stabilizing the structure, which resembles a beta-hairpin shape over a wide range of temperatures (283-313 K). Our results show that IG (42-61) possesses a well-organized three-dimensional structure stabilized by long-range hydrophobic interactions (Tyr50 ... Phe57 and Trp48 ... Val59) at T = 283 K and (Trp48 ... Val59) at 305 and 313 K. The mechanism of beta-hairpin folding and unfolding, as well as the influence of peptide length on its conformational properties, are also discussed.

Micellisation and immunoreactivities of dimeric β-caseins

Bovine β-casein (β-CN) is a highly amphiphilic micellising phospho-protein showing chaperone-like activity in vitro. Recently, existence of multiple sequential epitopes on β-CN polypeptide chain in both hydrophilic–polar (ψ) and hydrophobic–apolar domains (φ) has been evidenced. In order to clarify specific contribution of polar and apolar domains in micellisation process and in shaping immunoreactivity of β-CN, its dimeric/bi-amphiphilic “quasi palindromic” forms covalently connected by a disulfide bond linking either N-terminal (C4 β-CND) or C-terminal domain (C208 β-CND) were produced and studied. Depending on the C- or N-terminal position of inserted cysteine, each dimeric β-CN contains one polar/apolar region at the centre and two external hydrophobic/hydrophilic ends. Consequently, such casein dimers have radically different polarities/hydrophobicities on their outside surfaces. Dynamic light scattering (DLS) measurements indicate that these dimeric casein molecules form micelles of different sizes depending on arrangement of polar fragments of the β-CN mutants in their constrained dimers. Non-aggregated dimers have different hydrodynamic diameters that could be explained by their different geometries. Measurements of fluorescence showed more hydrophobic environment of Trp residues of C208 β-CND, while in similar experimental conditions Trp residues of C4 β-CND and native β-CN were more exposed to the polar medium. Both fluorescence and DLS studies showed greater propensity for micellisation of the dimeric β-CNs, suggesting that the factors inducing the formation of micelles are stronger in the bi-amphiphilic dimers. 1-Anilino-naphthalene-8-sulfonate (ANS) binding studies showed different binding of ANS by these dimers as well as different exposition of ANS binding (hydrophobic) regions in the micellar states. The differences in fluorescence resonance energy transfer (FRET) profiles of C4 β-CND and C208 β-CND can be explained by differences of distances and/or by differences of relative orientations of the donor (Trp) and acceptor (ANS), as well as by differences in quenching properties of the disulfide bridges and intra-molecular hydrophobic interactions. The immunoreactivity assays showed somewhat lower IgE response to C208 β-CND than to C4 β-CND. Thus, dimerization of C208 β-CN, connecting two C-terminal hydrophobic domains of two monomers doubling long-range hydrophobic interactions, possibly may hide a part of epitopes in the hydrophobic interface/core of C208 β-CND that is consistent with the results of DLS and fluorescence studies. The obtained results indicate structural differences of dimers – possibly the formation of Y- and U-shaped structures for C208 β-CND and C4 β-CND, respectively. This study not only demonstrated the importance of the organization of polar and hydrophobic regions during micellisation of the constrained and oriented β-CN dimers but also confirmed a possible role of C-terminal hydrophobic domain in the immunoreactivity profile of native β-CN.

Mechanism of formation of the C‐terminal β‐hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. II. Interplay of local backbone conformational dynamics and long‐range hydrophobic interactions in hairpin formation

Two peptides, corresponding to the turn region of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus, consisting of residues 51-56 [IG(51-56)] and 50-57 [IG(50-57)], respectively, were studied by circular dichroism and NMR spectroscopy at various temperatures and by differential scanning calorimetry. Our results show that the part of the sequence corresponding to the beta-turn in the native structure (DDATKT) of the B3 domain forms bent conformations similar to those observed in the native protein. The formation of a turn is observed for both peptides in a broad range of temperatures (T = 283-323 K), which confirms the conclusion drawn from our previous studies of longer sequences from the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G (16, 14, and 12 residues), that the DDATKT sequence forms a nucleation site for formation of the beta-hairpin structure of peptides corresponding to the C-terminal part of all the B domains of the immunoglobulin binding protein G. We also show and discuss the role of long-range hydrophobic interactions as well as local conformational properties of polypeptide chains in the mechanism of formation of the beta-hairpin structure.

Folding Mechanisms of Proteins with High Sequence Identity but Different Folds

The problem of how a protein folds from a linear chain of amino acids to the three-dimensional structure necessary for function is often investigated using proteins with a low degree of sequence identity that adopt different folds. The design of pairs of proteins with a high degree of sequence identity but different folds offers the opportunity for a complementary study; in two highly similar sequences, which residues are the most important in directing folding to a particular structure? Here we use molecular dynamics simulations to characterize the folding-unfolding pathways of a pair of proteins designed by Bryan and co-workers [Alexander, P. A., et al. (2005) Biochemistry 44, 14045-14054; He, Y. N., et al. (2005) Biochemistry 44, 14055-14061]. Despite being 59% identical, the two protein sequences fold to two different structures. The first sequence folds to the alpha+beta protein G structure and the second to the all-alpha-helical protein A structure. We show that the final protein structure is determined early along the folding pathway. In folding to the protein G structure, the single alpha-helix (alpha1) and the beta3-beta4 turn fold early. Formation of the hairpin turn essentially prevents folding to helical structure in this region of the protein. This early structure is then consolidated by formation of long-range hydrophobic interactions between alpha1 and the beta3-beta4 turn. The protein A sequence differs both in the residues that form the beta3-beta4 turn and also in many of the residues that form the early hydrophobic interactions in the protein G structure. Instead, in the protein A sequence, a more hierarchical mechanism is observed, with helices folding before many of the tertiary interactions are formed. We find that small, but critical, sequence differences determine the topology of the protein early along the folding pathway, which help to explain the process by which one fold can evolve into another.

Drying transition of confined water

Long-range hydrophobic interactions operating underwater are important in the mediation of many natural and synthetic phenomena, such as protein folding, adhesion and colloid stability. Here we show that rough hydrophobic surfaces can experience attractive forces over distances more than 30 times greater than any reported previously, owing to the spontaneous evaporation of the intervening, confined water. Our finding highlights the importance of surface roughness in the interaction of extended structures in water, which has so far been largely overlooked.

The three-dimensional structure of bovine calcium ion-bound osteocalcin using 1H NMR spectroscopy.

Structural information on osteocalcin or other noncollagenous bone proteins is very limited. We have solved the three-dimensional structure of calcium bound osteocalcin using (1)H 2D NMR techniques and proposed a mechanism for mineral binding. The protons in the 49 amino acid sequence were assigned using standard two-dimensional homonuclear NMR experiments. Distance constraints, dihedral angle constraints, hydrogen bonds, and (1)H and (13)C chemical shifts were all used to calculate a family of 13 structures. The tertiary structure of the protein consisted of an unstructured N terminus and a C-terminal loop (residues 16-49) formed by long-range hydrophobic interactions. Elements of secondary structure within residues 16-49 include type III turns (residues 20-25) and two alpha-helical regions (residues 27-35 and 41-44). The three Gla residues project from the same face of the helical turns and are surface exposed. The genetic algorithm-molecular dynamics simulation approach was used to place three calcium atoms on the NMR-derived structure. One calcium atom was coordinated by three side chain oxygen atoms, two from Asp30, and one from Gla24. The second calcium atom was coordinated to four oxygen atoms, two from the side chain in Gla 24, and two from the side chain of Gla 21. The third calcium atom was coordinated to two oxygen atoms of the side chain of Gla17. The best correlation of the distances between the uncoordinated Gla oxygen atoms is with the intercalcium distance of 9.43 A in hydroxyapatite. The structure may provide further insight into the function of osteocalcin.