Three-dimensional features of the bacterial polysaccharide (1 → 4)-β-D-glucuronan: A molecular modeling study

The mutant strain M5N1 CS of Rhizobium meliloti produces, in a Rhizobium complete medium supplemented with fructose and sucrose, a partially acetylated homopolymer of D -glucuronic acid residues linked β-(1 → 4). This polysaccharide forms thermoreversible gels with monovalent salts and thermally stable gels with divalent salts. In order to define the different levels of structural characterization, modeling simulations were performed for both the regular (1 → 4)-β-D -glucuronan and the acetylated derivatives. This required the evaluation of the accessible conformational space for the 16 disaccharides. Detailed conformational analysis was accomplished using the flexible residue of the MM3 molecular mechanics procedure and the results were used to access the configurational statistics of representative polysaccharide chains. Within the potential energy surfaces calculated for each disaccharide, several low energy conformers can be identified. When these conformations are extrapolated to regular polysaccharide structures, they generate polymers with right- and left-handed chirality along with a 2-fold axis. This later arrangement (n = 2, h = 5.16 Å) closely corresponds to that derived from a fiber x-ray diffraction investigation. The insertion of acetyl groups induces changes in the helical features of the polymer. As for the simulation of the configurational properties of (1 → 4)-β-D -glucuronan, an extended disordered chain having a persistence length of 105 Å (corresponding to 22 monomers) is predicted. This agrees with previous conclusions derived from solution study. The inclusion of varying amounts of acetyl groups only slightly perturbs the calculated persistence length. © 1998 John Wiley & Sons, Inc. Biopoly 45: 165–175, 1998     

Folding type-specific secondary structure propensities of amino acids,derived from α-helical, β-sheet, α/β, and α+β proteins of known structures

Folding type-specific secondary structure propensities of 20 naturally occurring amino acids have been derived from α-helical, β-sheet, α/β, and α+β proteins of known structures. These data show that each residue type of amino acids has intrinsic propensities in different regions of secondary structures for different folding types of proteins. Each of the folding types shows markedly different rank ordering, indicating folding type-specific effects on the secondary structure propensities of amino acids. Rigorous statistical tests have been made to validate the folding type-specific effects. It should be noted that α and β proteins have relatively small α-helices and β-strands forming propensities respectively compared with those of α+β and α/β proteins. This may suggest that, with more complex architectures than α and β proteins, α+β and α/β proteins require larger propensities to distinguish from interacting α-helices and β-strands. Our finding of folding type-specific secondary structure propensities suggests that sequence space accessible to each folding type may have differing features. Differing sequence space features might be constrained by topological requirement for each of the folding types. Almost all strong β-sheet forming residues are hydrophobic in character regardless of folding types, thus suggesting the hydrophobicities of side chains as a key determinant of β-sheet structures. In contrast, conformational entropy of side chains is a major determinant of the helical propensities of amino acids, although other interactions such as hydrophobicities and charged interactions cannot be neglected. These results will be helpful to protein design, class-based secondary structure prediction, and protein folding. © 1998 John Wiley & Sons, Inc. Biopoly 45: 35–49, 1998     

Energy minimization studies on α-turns

Using a grid search technique, the entire conformational space of a system of four linked peptide units (tetrapeptide) was scanned to pick out geometrically possible 5→1 type hydrogen-bonded conformations defined as an α-turn. The energy minimization of these conformations led to 23 distinct minimum energy conformations (MECs) falling in 13 different classes. The presence of β and γ turn type hydrogen bonds along with 5→1 type hydrogen bond gave conformational variability in a given class. The occurrence of bifurcated hydrogen bonding network was a characteristic feature of most of the MECs. In many prototype MECs non-glycyl residues such as Ala and Pro could be accommodated. Comparison of MECs with the α-turn examples that are observed in proteins showed that the conformationally worked out MECs occurred in isolation in proteins, with the α-helical α-turn being distinctly the most predominant. © 1998 European Peptide Society and John Wiley & Sons, Ltd.     

Design,synthesis and conformational analysis of hGM-CSF[13-31]-Gly-Pro-Gly-[103-116]

On the basis of the X-ray structure and results from structure--activity relationship studies, the following GM–CSF analogue was designed and synthesized by solid-phase methodology: hGM–CSF[13-31]-Gly-Pro-Gly-[103–116]-NH₂. This analogue was constructed to comprise helices A and D of the native hGM–CSF, covalently linked in an antiparallel orientation by the tripeptide spacer Gly-Pro-Gly, which is known as a turn-inducing sequence. The conformational analysis of the analogue by CD spectroscopy revealed an essentially random structure in water, while α-helix formation was observed upon addition of TFE. In 40% TFE the helix content was ∼45%. By two-dimensional NMR experiments in 1:1 water/trifluoroethanol mixture two helical sequences were identified comprising the segments corresponding to helix A and helix D. In addition to medium-range NOESY connectivities, a long-range cross-peak was found involving the leucine residues at positions 13 and 35. Based on the experimentally derived data (54 NOEs), the structure was refined by restrained molecular dynamics simulations over 120 ps at various temperatures. A representative conformation derived from the computer simulation is mainly characterized by two helical segments connected by a loop region. The overall three-dimensional structure of the analogue is comparable to the X-ray structure of hGM–CSF in that helices A and D are oriented in an antiparallel fashion, forming a two α-helix bundle. Nevertheless, there are small differences in the topology of the helices between the solution structure of the designed analogue and the X-ray structure of hGM–CSF. The possible implications of these conformational features at the effects of biological activity are discussed. © 1997 European Peptide Society and John Wiley & Sons, Ltd. J. Pep. Sci.3: 323–335 No. of Figures: 10. No. of Tables: 5. No. of References: 46     

Chemical cross-linking between lysine groups in vimentin oligomers is dependent on local peptide conformations

Previous studies have shown that cytoplasmic intermediate filaments, other than the keratins, are each constructed from a single type of polypeptide chain. Studies involving chemical crosslinking between lysine groups have shown that assembly of the filaments begins with the formation of dimers in which the peptide chains are parallel and in exact register, and that these dimers further associate in antiparallel patterns having specific degrees of overlap. In the present study, molecular modeling of the conformations of vimentin molecules indicated that lysine side chains in identical positions in regions of α-helix in parallel chains might be unable to be linked because they are on opposite sides of the coiled coil hydrophobic core. Examination of published data on chemical crosslinking of lysines in vimentin confirmed that there were no instances of linkage within dimers between the nine pairs of identical lysines that lie more than one position within α-helical regions in parallel chains. Even among linkages that apparently were between dimers, only one of the 11 linkage products identified involved lysines that were both within an α-helical region. In 10 of the 11 identified linkages between dimers, one or both of the linked lysines were in regions of random coil conformation. These results of molecular modeling indicate that relative motion between polypeptide chains in oligomers of intermediate filament proteins is not sufficient to overcome an orientation of lysine groups that is unfavorable for their chemical linkage. This finding supports the interpretations of keratin cross-linking data indicating that parallel homodimers are the basis for keratin intermediate filament assembly. © 1996 Wiley-Liss, Inc.     

Side-chain entropy effects on protein secondary structure formation

Loss of conformational entropy is one of the primary factors opposing protein folding. Both the backbone and side-chain of each residue in a protein will have their freedom of motion restricted in the final folded structure. The type of secondary structure of which a residue is part will have a significant impact on how much side-chain entropy is lost. Side-chain conformational entropies have previously been determined for folded proteins, simple models of unfolded proteins, alpha-helices, and a dipeptide model for beta-strands, but not for polyproline II (PII) helices. In this work, we present side-chain conformational estimates for the three regular secondary structure types: alpha-helices, beta-strands, and PII helices. Entropies are estimated from Monte Carlo computer simulations. Beta-strands are modeled as two structures, parallel and antiparallel beta-strands. Our data indicate that restraining a residue to the PII helix or antiparallel beta-strand conformations results in side-chain entropies equal to or higher than those obtained by restraining residues to the parallel beta-strand conformation. Side-chains in the alpha-helix conformation have the lowest side-chain entropies. The observation that extended structures retain the most side-chain entropy suggests that such structures would be entropically favored in unfolded proteins under folding conditions. Our data indicate that the PII helix conformation would be somewhat favored over beta-strand conformations, with antiparallel beta-strand favored over parallel. Notably, our data imply that, under some circumstances, residues may gain side-chain entropy upon folding. Implications of our findings for protein folding and unfolded states are discussed.     

Conformational changes due to vicinal glycosylation: The branched α-l-Rhap(1–2)[β-d-Galp(1–3)]-β-d-Glc1-OMe trisaccharide compared with its parent disaccharides*

Conformations of the α-l -Rhap(1-2)-β-d -Glc1-OMe and β-d -Galp(1-3)-β-d -Glc1-OMe disaccharides and the branched title trisaccharide were examined in DMSO-d₆ solution by ¹H-nmr. The distance mapping procedure was based on rotating frame nuclear Overhauser effect (NOE) constraints involving C- and O-linked protons, and hydrogen-bond constraints manifested by the splitting of the OH nmr signals for partially deuteriated samples. An “isotopomer-selected NOE” method for the unequivocal identification of mutually hydrogen-bonded hydroxyl groups was suggested. The length of hydrogen bonds thus detected is considered the only one motionally nonaveraged nmr-derived constraint. Molecular mechanics and molecular dynamics methods were used to model the conformational properties of the studied oligosaccharides. Complex conformational search, relying on a regular Φ,Ψ-grid based scanning of the conformational space of the selected glycosidic linkage, combined with simultaneous modeling of different allowed orientations of the pendant groups and the third, neighboring sugar residue, has been carried out. Energy minimizations were performed for each member of the Φ,Ψ grid generated set of conformations. Conformational clustering has been done to group the minimized conformations into families with similar values of glycosidic torsion angles. Several stable syn and anti conformations were found for the 1→2 and 1→3 bonds in the studied disaccharides. Vicinal glycosylation affected strongly the occupancy of conformational states in both branches of the title trisaccharide. The preferred conformational family of the trisaccharide (with average Φ,Ψ values of 38°, 17° for the 1→2 and 48°, 1° for the 1→3 bond, respectively) was shown by nmr to be stabilized by intramolecular hydrogen bonding between the nonbonded Rha and Gal residues. © 1998 John Wiley & Sons, Inc. Biopoly 46: 417–432, 1998     

The crystal structure of samarosporin I at atomic resolution

The atomic resolution structures of samarosporin I have been determined at 100 and 293 K. This is the first crystal structure of a natural 15‐residue peptaibol. The amino acid sequence in samarosporin I is identical to emerimicin IV and stilbellin I. Samarosporin is a peptide antibiotic produced by the ascomycetous fungus Samarospora rostrup and belongs to peptaibol subfamily 2. The structures at both temperatures are very similar to each other adopting mainly a 3₁₀‐helical and a minor fraction of α‐helical conformation. The helices are significantly bent and packed in an antiparallel fashion in the centered monoclinic lattice leaving among them an approximately 10‐Å channel extending along the crystallographic twofold axis. Only two ordered water molecules per peptide molecule were located in the channel. Comparisons have been carried out with crystal structures of subfamily 2 16‐residue peptaibols antiamoebin and cephaibols. The repercussion of the structural analysis of samarosporin on membrane function is discussed. Copyright © 2012 European Peptide Society and John Wiley & Sons, Ltd.     

A priori crystal structure prediction of native celluloses

The packing of beta-1,4-glucopyranose chains has been modeled to further elaborate the molecular structures of native cellulose microfibrils. A chain pairing procedure was implemented that evaluates the optimal interchain distance and energy for all possible settings of the two chains. Starting with a rigid model of an isolated chain, its interaction with a second chain was studied at various helix-axis translations and mutual rotational orientations while keeping the chains at van der Waals separation. For each setting, the sum of the van der Waals and hydrogen-bonding energy was calculated. No energy minimization was performed during the initial screening, but the energy and interchain distances were mapped to a three-dimensional grid, with evaluation of parallel settings of the cellulose chains. The emergence of several energy minima suggests that parallel chains of cellulose can be paired in a variety of stable orientations. A further analysis considered all possible parallel arrangements occurring between a cellulose chain pair and a further cellulose chain. Among all the low-energy three-chain models, only a few of them yield closely packed three-dimensional arrangements. From these, unit-cell dimensions as well as lattice symmetry were derived; interestingly two of them correspond closely to the observed allomorphs of crystalline native cellulose. The most favorable structural models were then optimized using a minicrystal procedure in conjunction with the MM3 force field. The two best crystal lattice predictions were for a triclinic (P(1)) and a monoclinic (P2(1)) arrangement with unit cell dimensions a = 0.63, b = 0.69, c = 1.036 nm, alpha = 113.0, beta = 121.1, gamma = 76.0 degrees, and a = 0.87, b = 0.75, c = 1.036 nm, gamma = 94.1 degrees, respectively. They correspond closely to the respective lattice symmetry and unit-cell dimensions that have been reported for cellulose Ialpha and cellulose Ibeta allomorphs. The suitability of the modeling protocol is endorsed by the agreement between the predicted and experimental unit-cell dimensions. The results provide pertinent information toward the construction of macromolecular models of microfibrils.     

Chain-length dependence of alpha-helix to beta-sheet transition in polylysine: model of protein aggregation studied by temperature-tuned FTIR spectroscopy

The chain-length dependence of the alpha-helix to beta-sheet transition in poly(L-lysine) is studied by temperature-tuned FTIR spectroscopy. This study shows that heterogeneous samples of poly(L-lysine), comprising polypeptide chains with various lengths, undergo the alpha-beta transition at an intermediate temperature compared to homogeneous ingredients. This holds true as long as each individual fraction of the polypeptide is capable of adopting an antiparallel beta-sheet structure. The tendency is that the longer chain is, the lower the alpha-beta transition temperature is, which has been linked to the presence of distorted or solvated helices with turns or beta sheets in elongating chains of poly(L-lysine). As such helical structures are apparently conducive to the alpha-beta transition, this draws a comparison to the hypothesis of metastable protein conformational states being a common stage in amyloid-formation pathways. The antiparallel architecture of the beta sheet is likely to reflect the pretransition interhelical interactions in poly(L-lysine). Namely, the chains are arranged in an antiparallel manner because of energetically favored antiparallel pre-assembly of dipolar alpha helices.     

Signature of n→π* interactions in α-helices

The oxygen of a peptide bond has two lone pairs of electrons. One of these lone pairs is poised to interact with the electron-deficient carbon of the subsequent peptide bond in the chain. Any partial covalency that results from this n→π* interaction should induce pyramidalization of the carbon (C'(i)) toward the oxygen (O(i-1)). We searched for such pyramidalization in 14 peptides that contain both α- and β-amino acid residues and that assume a helical structure. We found that the α-amino acid residues, which adopt the main chain dihedral angles of an α-helix, display dramatic pyramidalization but the β-amino acid residues do not. Thus, we conclude that O(i-1) and C'(i) are linked by a partial covalent bond in α-helices. This finding has important ramifications for the folding and conformational stability of α-helices in isolation and in proteins.     

Structural properties of amyloid β(1‐40) dimer explored by replica exchange molecular dynamics simulations

Replica exchange molecular dynamics simulations (300 ns) were used to study the dimerization of amyloid β(1‐40) (Aβ(1‐40)) polypeptide. Configurational entropy calculations revealed that at physiological temperature (310 K, 37°C) dynamic dimers are formed by randomly docked monomers. Free energy of binding of the two chains to each other was ?93.56 ± 6.341 kJ mol^?1. Prevalence of random coil conformations was found for both chains with the exceptions of increased β‐sheet content from residues 16‐21 and 29‐32 of chain A and residues 15‐21 and 30‐33 of chain B with β‐turn/β‐bend conformations in both chains from residues 1‐16, 21‐29 of chain A, 1‐16, and 21‐29 of chain B. There is a mixed β‐turn/β‐sheet region from residues 33‐38 of both chains. Analysis of intra‐ and interchain residue distances shows that, although the individual chains are highly flexible, the dimer system stays in a loosely packed antiparallel β‐sheet configuration with contacts between residues 17‐21 of chain A with residues 17‐21 and 31‐36 of chain B as well as residues 31‐36 of chain A with residues 17‐21 and 31‐36 of chain B. Based on dihedral principal component analysis, the antiparallel β‐sheet‐loop‐β‐sheet conformational motif is favored for many low energy sampled conformations. Our results show that Aβ(1‐40) can form dynamic dimers in aqueous solution that have significant conformational flexibility and are stabilized by collapse of the central and C‐terminal hydrophobic cores with the expected β‐sheet‐loop‐β‐sheet conformational motif. Proteins 2017; 85:1024–1045. © 2017 Wiley Periodicals, Inc.     

Alpha helix capping in synthetic model peptides by reciprocal side chain–main chain interactions: Evidence for an N terminal “capping box”

A significant fraction of the amino acids in proteins are alpha helical in conformation. Alpha helices in globular proteins are short, with an average length of about twelve residues, so that residues at the ends of helices make up an important fraction of all helical residues. In the middle of a helix, H-bonds connect the NH and CO groups of each residue to partners four residues along the chain. At the ends of a helix, the H-bond potential of the main chain remains unfulfilled, and helix capping interactions involving bonds from polar side chains to the NH or CO of the backbone have been proposed and detected. In a study of synthetic helical peptides, we have found that the sequence Ser-Glu-Asp-Glu stabilizes the alpha helix in a series of helical peptides with consensus sequences. Following the report by Harper and Rose, which identifies SerXaaXaaGlu as a member of a class of common motifs at the N termini of alpha helices in proteins that they refer to as “capping boxes,” we have reexamined the side chain–main chain interactions in a varient sequence using ¹H NMR, and find that the postulated reciprocal side chain-backbone bonding between the first Ser and last Glu side chains and their peptide NH partners can be resolved: Deletion of two residues N terminal to the Ser-Glu-Asp-Glu sequence in these peptides has no effect on the initiation of helical structure, as defined by two-dimensional (2D) NMR experiments on this variant. Thus the capping box sequence Ser-Glu-Asp-Glu inhibits N terminal fraying of the N terminus of alpha helix in these peptides, and shows the side chain–main chain interactions proposed by Harper and Rose. It thus acts as a helix initiating signal. Since normal a helix cannot propagate beyond the N terminus of this structure, the box acts as a termination signal in this direction as well. © 1994 John Wiley & Sons, Inc.     

Peptides containing the sulfonamide junction: Synthesis,structure, and conformation of Z-Tau-Pro-Phe-NHiPr

The taurine (Tau) containing tripeptide derivative Z-Tau-Pro-Phe-NHiPr (1) has been synthesized as suitable sulfonamido-pseudopeptide model to investigate formation and conformational properties of folded secondary structures stabilized by intramolecular H bonds directly involving the sulfonamide junction. In the crystal the pseudopeptide 1 adopts a type I β-turn with the Pro and Phe residues located at the (i + 1) and (i + 2) corner positions, respectively. The turn is stabilized by a 4 → 1 H bond engaging one of the SO₂ oxygen atoms and the isopropylamide NH. In CDCl₃ solution the β-turn folding is accompanied by a γ-turn centered at the Pro and involving a 3 → 1 H bond between the SO₂ and the Phe NH. A comparison of the structural and conformational properties found in 1 with those of the already known sulfonamido-pseudopeptides, with particular reference to the models containing the Tau-Pro junction, is also reported. © 1997 John Wiley & Sons, Inc. Biopoly 41: 555–567, 1997.     

OCCURRENCE AND CHARACTERIZATION OF ARABINOGALACTAN‐LIKE PROTEINS AND HEMICELLULOSES IN MICRASTERIAS (STREPTOPHYTA)1

The cell wall of the green alga Micrasterias denticulata Bréb. ex Ralfs (Desmidiaceae, Zygnematophyceae, Streptophyta) was investigated to obtain information on the composition of component polysaccharides and proteoglycans to allow comparison with higher plants and to understand cell wall functions during development. Various epitopes currently assigned to arabinogalactan‐proteins (AGPs) of higher plants could be detected in Micrasterias by immuno TEM and immunofluorescence methods, but the walls did not bind the β‐d ‐glycosyl‐Yariv (β‐GlcY) reagent. Secretory vesicles and the primary wall were labeled by antibodies against AGPs (JIM8, JIM13, JIM14). Dot and Western blot experiments indicated a proteoglycan nature of the epitopes recognized, which consisted of galactose and xylose as major sugars by high performance anion exchange chromatography with pulsed amperometric detection (HPAEC‐PAD). Epitopes of alkali‐soluble polysaccharides assigned to noncellulosic polysaccharides in higher plants could be detected and located in the wall during its formation. The polyclonal anti‐xyloglucan (anti‐XG) antibody labeled primary and secondary wall of Micrasterias, whereas the monoclonal antibody CCRC‐M1, directed against the fucose/galactose side chain of xyloglucan (XyG), did not recognize any structures. Labeling by anti‐XG antibody at the trans‐sites of the dictyosomes and at wall material containing vesicles indicated that secretion of the epitopes occurred similar to higher plants. The presence of (1→3, 1→4)‐β‐glucan (mixed linked glucan) in the secondary cell wall but not in the primary cell wall of Micrasterias could be demonstrated by an antibody recognizing this glucan type, whereas (1→3)‐β‐glucan (callose) could not be detected. The analytical results revealed that alkali‐soluble polysaccharides in the secondary wall of Micrasterias consist mostly of (1→3, 1→4)‐β‐d ‐glucan.     

Variable chain conformations of renatured β‐glucan in dimethylsulfoxide/water mixture

We have firstly demonstrated the renaturation process of dissociated single chains of lentinan (s‐LNT) and the variable conformations of the renatured LNT (r‐LNT). The results from ultrasensitive differential scanning calorimetry and circular dichroism revealed that the variable structures including perfect triple helix, defective triple helix containing duplex segment, and single chains occurred in the renaturation of s‐LNT, depending on the renaturation time, solvent composition, molecular weight, and the mode of renaturation. When water was added into s‐LNT/dimethylsulfoxide (DMSO) to reach 95% (v/v), the classic low‐temperature intra‐triple‐helical conformational transition at ～10^°C (T₁) appeared within 4 h, indicative of a rapid reconstruction of triple helical structure. Besides, one newly endothermic peak at ～43^°C (T₂) simultaneously occurred, which was first ascribed to the melting of duplex segment in the imperfect triplex. The duplex stretches disappeared when DMSO reached 50%, in which single chains coexisted with triplex. Moreover, the duplex segment disappeared by slowly dropping water into s‐LNT/DMSO. This work suggested that the structure of r‐LNT could be controllable, and provided important information for their successful development and application in polymer and life science. © 2012 Wiley Periodicals, Inc. Biopolymers 97:988–997, 2012.     

Conformational analysis of protein structures derived from NMR data

A study is presented of the conformational characteristics of NMR-derived protein structures in the Protein Data Bank compared to X-ray structures. Both ensemble and energy-minimized average structures are analyzed. We have addressed the problem using the methods developed for crystal structures by examining the distribution of ?, Ψ, and χ angles as indicators of global conformational irregularity. All these features in NMR structures occur to varying degrees in multiple conformational states. Some measures of local geometry are very tightly constrained by the methods used to generate the structure, e.g., proline ? angles, α-helix ?, Ψ angles, ω angles, and C_α chirality. The more lightly restrained torsion angles do show increasead clustering as the number of overall experimental observations increases. ?, Ψ, and χ₁ angle conformational heterogeneity is strongly correlated with accessibility but shows additional differences which reflect the differing number of observations possible in NMR for the various side chains (e.g., many for Trp, few for Ser). In general, we find that the core is defined to a notional resolution of 2.0 to 2.3 Å. Of real interest is the behavior of surface residues and in particular the side chains where multiple rotameric states in different structures can vary from 10% to 88%. Later generation structures show a much tighter definition which correlates with increasing use of J-coupling information, stereospecific assignments, and heteronumclear techniques. A suite of programs is being developed to address the special needs of NMR-derived structures which will take into account the existence of increased mobility in solution. © 1993 Wiley-Liss, Inc.     

Effect of external electrostatic field on the stability of β sheet structures

To explore the effect of an external electrostatic field (EEF) on the stability of protein conformations, the molecular dynamic modeling approach was applied to evaluate the effect of an EEF along the x or y direction on a water cluster containing a parallel or antiparallel β sheet structure. The β sheet structure contained two strands with a (Gly)₃ sequence separated by a distance d along the x direction. The mean forces between the two strands along the x direction were computed from the trajectories of molecular dynamics simulations. In the absence of the EEF, the forces between the two strands in vacuum were repulsive and attractive in the parallel and antiparallel β sheet structures, respectively. In contrast, the mean forces between the two strands in water were attractive in both the parallel and antiparallel β sheet structures. This is because the electric interactions between the two strands were shielded by water, and the hydrophobic effect dominated the interaction between the two strands. When an EEF >50 MV/cm was applied to the water cluster, the attractive force between the two strands in the parallel and antiparallel β sheet structures decreased and increased, respectively. Further, the binding affinity between the two strands in the parallel and antiparallel β sheet structures also decreased and increased, respectively. This is because the large EEF leads to dielectric saturation, and consequently reduces the effects of the dielectric shielding and hydrophobic interactions. © 2014 Wiley Periodicals, Inc. Biopolymers 101: 861–870, 2014.