Importance of chirality and reduced flexibility of protein side chains: a study with square and tetrahedral lattice models

Side chains of amino acid residues are the determining factor that distinguishes proteins from other unstable chain polymers. In simple models they are often represented implicitly (e.g., by spin states) or simplified as one atom. Here we study side chain effects using two-dimensional square lattice and three-dimensional tetrahedral lattice models, with explicitly constructed side chains formed by two atoms of different chirality and flexibility. We distinguish effects due to chirality and effects due to side chain flexibilities, since residues in proteins are L residues, and their side chains adopt different rotameric states. For short chains, we enumerate exhaustively all possible conformations. For long chains, we sample effectively rare events such as compact conformations and obtain complete pictures of ensemble properties of conformations of these models at all compactness region. This is made possible by using sequential Monte Carlo techniques based on chain growth method. Our results show that both chirality and reduced side chain flexibility lower the folding entropy significantly for globally compact conformations, suggesting that they are important properties of residues to ensure fast folding and stable native structure. This corresponds well with our finding that natural amino acid residues have reduced effective flexibility, as evidenced by statistical analysis of rotamer libraries and side chain rotatable bonds. We further develop a method calculating the exact side chain entropy for a given backbone structure. We show that simple rotamer counting underestimates side chain entropy significantly for both extended and near maximally compact conformations. We find that side chain entropy does not always correlate well with main chain packing. With explicit side chains, extended backbones do not have the largest side chain entropy. Among compact backbones with maximum side chain entropy, helical structures emerge as the dominating configurations. Our results suggest that side chain entropy may be an important factor contributing to the formation of alpha helices for compact conformations.     

Ab initio polypeptide structure prediction

The biological activity of a polypeptide strongly depends on its 3D structure. Ab initio prediction of the native structure from the sequence of amino acids has long motivated the development of an optimum energy model such that interactions present in the native conformation are stronger than those present in nonnative conformations and of algorithms capable of finding the basin of lowest free energy among an astronomically large number of possible conformations. Despite recent progress in our understanding of the factors responsible for both polypeptide stability and formation, computer simulations of polypeptide models are still far from being practical software tools for biologists. In this work, state-of-the-art computer simulations aimed at ab initio structure prediction in aqueous solution are reviewed and their strengths and weaknesses are highlighted. Received: 23 June 1999 / Accepted: 20 September 1999 / Published online: 15 December 1999     

Exploration of the relationship between topology and designability of conformations

Protein structures are evolutionarily more conserved than sequences, and sequences with very low sequence identity frequently share the same fold. This leads to the concept of protein designability. Some folds are more designable and lots of sequences can assume that fold. Elucidating the relationship between protein sequence and the three-dimensional (3D) structure that the sequence folds into is an important problem in computational structural biology. Lattice models have been utilized in numerous studies to model protein folds and predict the designability of certain folds. In this study, all possible compact conformations within a set of two-dimensional and 3D lattice spaces are explored. Complementary interaction graphs are then generated for each conformation and are described using a set of graph features. The full HP sequence space for each lattice model is generated and contact energies are calculated by threading each sequence onto all the possible conformations. Unique conformation giving minimum energy is identified for each sequence and the number of sequences folding to each conformation (designability) is obtained. Machine learning algorithms are used to predict the designability of each conformation. We find that the highly designable structures can be distinguished from other non-designable conformations based on certain graphical geometric features of the interactions. This finding confirms the fact that the topology of a conformation is an important determinant of the extent of its designability and suggests that the interactions themselves are important for determining the designability.     

Helix‐coil and beta sheet‐coil transitions in a simplified,yet realistic protein model

A reduced model of polypeptide chains and protein stochastic dynamics is employed in Monte Carlo studies of the coil‐globule transition. The model assumes a high‐resolution lattice representation of protein conformational space. The interaction scheme is derived from a statistical analysis of structural regularities seen in known three‐dimensional protein structures. It is shown that model polypeptides containing residues that have strong propensities towards locally expanded conformations collapse to β‐like globular conformations, while polypeptides containing residues with helical propensities form globules of closely packed helices. A more cooperative transition is observed for β‐type systems. It is also demonstrated that hydrogen bonding is an important factor for protein cooperativity, although, for systems with suppressed hydrogen bond interactions, a higher cooperativity of β‐type proteins is also observed.     

Synthesis and Luminescent Properties of Two Zinc(II) Coordination Polymers Constructed by 4‐(Pyridin‐4‐ylmethoxy)benzolic Acid Ligand

Two coordination polymers, namely [Zn(L)Cl] ( 1 ) and [Zn(L)₂] ( 2 ) [L = 4‐(pyridin‐4‐ylmethoxy)benzolic acid] were synthesized under hydrothermal conditions and characterized by single‐crystal X‐ray diffraction analyses, powder X‐ray diffraction, and thermogravimetric analysis. Compounds 1 and 2 have a two‐dimensional square‐shaped structure (the dimensions are 15.43 × 15.43 Å for 1 and 12.064 × 15.017 Å for 2 ) with (4⁴ · 6²) topology. Moreover, compounds 1 and 2 exhibit a 3D supramolecular structure made up by strong π–π interactions from the adjacent layers. Furthermore, compounds 1 and 2 show good fluorescence properties in the solid state at room temperature.     

Generation and enumeration of compact conformations on the two-dimensional triangular and three-dimensional fcc lattices

We enumerated all compact conformations within simple geometries on the two-dimensional (2D) triangular and three-dimensional (3D) face centered cubic (fcc) lattice. These compact conformations correspond mathematically to Hamiltonian paths and Hamiltonian circuits and are frequently used as simple models of proteins. The shapes that were studied for the 2D triangular lattice included mxn parallelograms, regular equilateral triangles, and various hexagons. On the 3D fcc lattice we generated conformations for a limited class of skewed parallelepipeds. Symmetries of the shape were exploited to reduce the number of conformations. We compared surface to volume ratios against protein length for compact conformations on the 3D cubic lattice and for a selected set of real proteins. We also show preliminary work in extending the transfer matrix method, previously developed by us for the 2D square and the 3D cubic lattices, to the 2D triangular lattice. The transfer matrix method offers a superior way of generating all conformations within a given geometry on a lattice by completely avoiding attrition and reducing this highly complicated geometrical problem to a simple algebraic problem of matrix multiplication.     

A comparative study of two polymorphs of L‐aspartic acid hydrochloride

Two polymorphs of L‐aspartic acid hydrochloride, C₄H₈NO₄⁺·Cl⁻, were obtained from the same aqueous solution. Their crystal structures have been determined from single‐crystal data collected at 100 K. The crystal structures revealed three‐ and two‐dimensional hydrogen‐bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N—H...Cl and O—H...Cl interactions and form alternating cation–anion layer‐like structures. The two polymorphs share common structural features; however, the conformations of the L‐aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.     

A Three‐Dimensional Porous Organic Semiconductor Based on Fully sp2‐Hybridized Graphitic Polymer

Dimensionality plays an important role in the charge transport properties of organic semiconductors. Although three‐dimensional semiconductors, such as Si, are common in inorganic materials, imparting electrical conductivity to covalent three‐dimensional organic polymers is challenging. Now, the synthesis of a three‐dimensional π‐conjugated porous organic polymer (3D p‐POP) using catalyst‐free Diels–Alder cycloaddition polymerization followed by acid‐promoted aromatization is presented. With a surface area of 801 m² g^?1, full conjugation throughout the carbon backbone, and an electrical conductivity of 6(2)×10^?4 S cm^?1 upon treatment with I₂ vapor, the 3D p‐POP is the first member of a new class of permanently porous 3D organic semiconductors.     

Triptycene‐Derived Calix[6]arenes: Synthesis,Structures, and Their Complexation with Fullerenes C60 and C70

Two pairs of novel triptycene‐derived calix[6]arenes 4 a , b and 5 a , b have been efficiently synthesized through both one‐pot and two‐step fragment‐coupling strategies starting from 2,7‐bis(hydroxymethyl)‐1,8‐dimethoxytriptycene 1 . Subsequent demethylation of 4 a , b and 5 a , b with BBr₃ in dry dichloromethane gave the macrocyclic compounds 6 a , b and 7 a , b . Treatment of either 4 a or 6 a with AlCl₃ resulted in the same debutylated product 8 , while 9 was similarly obtained from either 5 a or 7 a . Structural studies revealed that all of the macrocycles have well‐defined structures with fixed conformations both in solution and in the solid state owing to the introduction of the triptycene moiety with a rigid three‐dimensional (3D) structure, making them very different from their classical calix[6]arene counterparts. As a consequence, it was found that all of these the triptycene‐derived calix[6]arenes could encapsulate small neutral molecules in their cavities in the solid state. Moreover, it was also found that the macrocycles 4 b and 5 b showed highly efficient complexation abilities toward fullerenes C₆₀ and C₇₀, forming 1:1 complexes with association constants ranging from (5.22±0.20)×10⁴ to (8.68±0.30)×10⁴ M ^?1.     

Chiral oxazoline substituted optically active poly(m‐phenylene)s: Synthesis and coupling polymerizations of (S)‐4‐benzyl‐2‐(3,5‐dihalidephenyl) oxazoline using transition metal catalysts

Optically active poly(m‐phenylene)s substituted with chiral oxazoline derivatives have been synthesized by the nickel‐catalyzed Yamamoto coupling reaction of optically active (S)‐4‐benzyl‐2‐(3,5‐dihalidephenyl)oxazoline derivatives (X = Br or I). The structures and chiroptical properties of the polymers were characterized by spectroscopic methods and thermal gravimetric analyses. The polymers showed higher absolute optical specific rotation values than their corresponding monomer, and showed a Cotton effect at transition region of conjugated main chain. The optical activities of the polymers should be attributed to the higher order structure such as helical conformations. Moreover, the helical conformation could be induced by addition of metal salts into polymer solutions. The polymers showed good thermal stabilities, which was attributable to the oxazoline side chains. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2013     

2‐(2‐Naphthyloxy)acetate derivatives. I. A new class of antiamnesic agents

The title compounds 1‐(2‐naphthyloxymethylcarbonyl)piperidine, C₁₇H₁₉NO₂, (I), and 3‐methyl‐1‐(2‐naphthyl­oxy­methyl­carbonyl)­piperidine, C₁₈H₂₁NO₂, (II), are potential antiamnesics. In (II), the methyl‐substituted piperidine ring is disordered over two conformations. The piperidine ring has a chair conformation in both compounds. In (I), the mol­ecules are linked by weak intermolecular C—H⃛O interactions to give networks represented by C(4), C(6) and (18) graph‐set motifs, while in (II), weak intermolecular C—H⃛O interactions generate (5), C(4) and C(7) graph‐set motifs. The dihedral angle between the naphthalene moiety and the piperidine ring is 33.83 (7)° in (I), while it is 31.78 (11) and 19.38 (19)° for the major and minor conformations, respectively, in (II).     

二维HP格点模型中的紧密高分子链构象及其热力学性质的研究

采用二维HP模型用精确计数法和MonteCarlo方法研究了链长为N(≤ 2 2 )的紧密高分子链的构象和热力学性质 .发现不同HP序列的紧密高分子链的平均自由能和平均配分函数与链长N存在关系 :〈F〉=aN+b ,　ln〈Z〉=a′N +b′ .同时发现对于可折叠成基态且简并度为 1的紧密高分子链 ,其平均自由能和平均配分函数与链长N也存在相似的关系 .在HP模型中对于链长为N的紧密高分子链 ,存在着 2 N + 1 个不同的HP序列 .我们发现可以折叠成基态且简并度为 1的蛋白质分子的HP序列数目NS 为NS =a× 2 N+ 1 　 (a =0 0 2 5 ) ,对应的HP序列中 ,疏水基团 (H)数目的含量为 4 0 %～ 6 0 %的序列出现的几率最大 .同时在这些紧密高分子链中有些具有相同的结构 ,发现结构的‘简并度’为 3 3～ 4 0 (10≤N≤ 16 ) .在紧密高分子链折叠过程中 ,折叠的初期能量下降比较快 ,折叠的中期能量下降比较缓慢 ,折叠的后期能量下降也是比较快     

Three isostructural solvates of a tetrahydrofurochromenone derivative

Isostructurality is more likely to occur in multicomponent systems. In this context, three closely related solvates were crystallized, namely, benzene (C₂₇H₂₁BrO₆·C₆H₆), toluene (C₂₇H₂₁BrO₆·C₇H₈) and xylene (C₂₇H₂₁BrO₆·C₈H₁₀) with methyl 3a‐acetyl‐3‐(4‐bromophenyl)‐4‐oxo‐1‐phenyl‐3,3a,4,9b‐tetrahydro‐1H‐furo[3,4‐c ]chromene‐1‐carboxylate, and their crystal structures determined. All three structures belong to the same space group (P ) and display similar unit‐cell dimensions and conformations, as well as isostructural crystal packings. The isostructurality is confirmed by unit‐cell and isostructural similarity indices. In each solvate, weak C—H…O and C—H…π interactions extend the molecules into two‐dimensional networks, which are further linked by C—H…Br and Br…Br interactions into three‐dimensional networks. The conformation of the core molecule is predominantly responsible for governing the isostructurality.     

4′‐Iodo‐2,2′:6′,2′′‐terpyridine

In the nearly planar title compound, C₁₅H₁₀IN₃, the three pyridine rings exhibit transoid conformations about the interannular C—C bonds. Very weak C—H...N and C—H...I interactions link the molecules into ribbons. Significant π–π stacking between molecules from different ribbons completes a three‐dimensional framework of intermolecular interactions. Four different packing motifs are observed among the known structures of simple 4′‐substituted terpyridines.     

Constraining Cyclic Peptides To Mimic Protein Structure Motifs

Many proteins exert their biological activities through small exposed surface regions called epitopes that are folded peptides of well‐defined three‐dimensional structures. Short synthetic peptide sequences corresponding to these bioactive protein surfaces do not form thermodynamically stable protein‐like structures in water. However, short peptides can be induced to fold into protein‐like bioactive conformations (strands, helices, turns) by cyclization, in conjunction with the use of other molecular constraints, that helps to fine‐tune three‐dimensional structure. Such constrained cyclic peptides can have protein‐like biological activities and potencies, enabling their uses as biological probes and leads to therapeutics, diagnostics and vaccines. This Review highlights examples of cyclic peptides that mimic three‐dimensional structures of strand, turn or helical segments of peptides and proteins, and identifies some additional restraints incorporated into natural product cyclic peptides and synthetic macrocyclic peptidomimetics that refine peptide structure and confer biological properties.     

Syntheses,Crystal Structures,and Cytotoxicity Evaluation of two Chain‐like and Diamond‐like Silver(I) Complexes

Two coordination polymers [Ag(dach)]_n(NO₃)_n ( 1 ) and [Ag(teda)(F₃CSO₃)]_n ( 2 ) (dach = 1, 2‐diaminocyclohexane, teda = 1, 4‐diazabicyclo[2.2.2]octane) have been synthesized and characterized by X‐ray single crystal analysis and cytotoxicity investigation. Compound 1 has a one‐dimensional chain‐like structure which is extended by ligand unsupported Ag···Ag interactions, hydrophobic interaction and hydrogen bonds into a three‐dimensional supramolecular array while compound 2 shows three‐dimensional diamond‐like framework constructed by coordination bonds. The high cytotoxities of these two compounds imply that they are potential candidates for antitumor agents.     

Synthesis and photovoltaic properties of two‐dimensional D‐A copolymers with conjugated side chains

Four novel two‐dimensional (2D) donor–acceptor (D‐A) type copolymers with different conjugated side chains, P1 , P2 , P3 , and P4 (see Fig. 1 ), are designed and synthesized for the application as donor materials in polymer solar cells (PSCs). To the best of our knowledge, there were few reports to systematically study such 2D polymers with D‐A type main chains in this area. The optical energy band gaps are about 2.0 eV for P1 – P3 and 1.67 eV for P4 . PSC devices using P1 – P4 as donor and [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester as acceptor in a weight ratio of 1:3 were fabricated and characterized to investigate the photovoltaic properties of the polymers. Under AM 1.5 G, 100 mA/cm² illumination, a high open‐circuit voltage (V_oc) of 0.9 V was recorded for P3 ‐based device due to its low HOMO level, and moderate fill factor was obtained with the best value of 58.6% for P4 ‐based device, which may mainly be the result of the high hole mobility of the polymers (up to 1.82 × 10^?3 cm²/V s). © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011     

Study of Self‐Assembly of the Lignin Model Compound on Cellulose Model Substrate

Herein we report a topographical study of the supramolecular organization of enzymatically polymerized lignin model compound – dehydrogenative polymer (DHP) of coniferyl alcohol – on cellulose substrate, using the Environmental Scanning Electron Microscopic (ESEM) technique. A comparison of deposits obtained by bulk polymerization in solution and direct polymerization in the presence of cellulose substrate shows distinct differences in supramolecular organization. DHP polymerized in solution expresses a 3‐D structure with short‐range ordered motifs, while the polymer formed in the presence of cellulose substrate arranges in a single layer compact structure consisting of several domains. Such structures could be described as a two‐dimensional hexagonal close packed lattice(HCPL), with the dimension of unit cell in 1 μm range. The domains have a quite regular structure with few lattice defects, forming a good example of two‐dimensional colloidal crystal. The growth of DHP globules and their assembly into supramolecular structures are interpreted in terms of cooperative electrostatic interaction of polymer precursors, with a framework of cellulose OH groups and interfacial interactions (hydrophilic/hydrophobic) in the course of the structure growth. The results strongly suggest that the carbohydrate matrix in plant cells can serve as a template for lignin structure formation in the plant cell wall.

Self‐assembled lignin model compound on cellulose substrate.