Side-chain dynamics and protein folding

The processes by which protein side chains reach equilibrium during a folding reaction are investigated using both lattice and all-atom simulations. We find that rates of side-chain relaxation exhibit a distribution over the protein structure, with the fastest relaxing side chains located in positions kinetically important for folding. Traversal of the major folding transition state corresponds to the freezing of a small number of side chains, belonging to the folding nucleus, whereas the rest of the protein proceeds toward equilibrium via backbone fluctuations around the native fold. The postnucleation processes by which side chains relax are characterized by very slow dynamics and many barrier crossings, and thus resemble the behavior of a glass.     

Highly potent side-chain to side-chain cyclized enkephalin analogues containing a carbonyl bridge: synthesis, biology and conformation.

Six novel cyclic enkephalin analogues have been synthesized. Cyclization of the linear peptides containing basic amino acid residues in position 2 and 5 was achieved by treatment with bis(4-nitrophenyl)carbonate. It was found that some of the compounds exibit unusually high mu-opioid activity in the guinea pig ileum (GPI) assay. The 18-membered analogue cyclo(N(epsilon),N(beta)-carbonyl-D-Lys2,Dap5)-enkephalinamide turned out to be one of the most potent mu-agonists reported so far. NMR spectra of the peptides were recorded and structural parameters were determined. The conformational space was exhaustively examined for each of them using the electrostatically driven Monte Carlo method. Each peptide was finally described as an ensemble of conformations. A model of the bioactive conformation of this class of opioid peptides was proposed.     

Analysis of a data set of paired uncomplexed protein structures: new metrics for side-chain flexibility and model evaluation

We compiled and analyzed a data set of paired protein structures containing proteins for which multiple high-quality uncomplexed atomic structures were available in the Protein Data Bank. Side-chain flexibility was quantified, yielding a set of residue- and environment-specific confidence levels describing the range of motion around chi1 and chi2 angles. As expected, buried residues were inflexible, adopting similar conformations in different crystal structure analyses. Ile, Thr, Asn, Asp, and the large aromatics also showed limited flexibility when exposed on the protein surface, whereas exposed Ser, Lys, Arg, Met, Gln, and Glu residues were very flexible. This information is different from and complementary to the information available from rotamer surveys. The confidence levels are useful for assessing the significance of observed side-chain motion and estimating the extent of side-chain motion in protein structure prediction. We compare the performance of a simple 40 degrees threshold with these quantitative confidence levels in a critical evaluation of side-chain prediction with the program SCWRL.     

Fast and accurate side-chain topology and energy refinement (FASTER) as a new method for protein structure optimization

We have developed an original method for global optimization of protein side-chain conformations, called the Fast and Accurate Side-Chain Topology and Energy Refinement (FASTER) method. The method operates by systematically overcoming local minima of increasing order. Comparison of the FASTER results with those of the dead-end elimination (DEE) algorithm showed that both methods produce nearly identical results, but the FASTER algorithm is 100-1000 times faster than the DEE method and scales in a stable and favorable way as a function of protein size. We also show that low-order local minima may be almost as accurate as the global minimum when evaluated against experimentally determined structures. In addition, the new algorithm provides significant information about the conformational flexibility of individual side-chains. We observed that strictly rigid side-chains are concentrated mainly in the core of the protein, whereas highly flexible side-chains are found almost exclusively among solvent-oriented residues.     

Assessment of protein side‐chain conformation prediction methods in different residue environments

Computational prediction of side‐chain conformation is an important component of protein structure prediction. Accurate side‐chain prediction is crucial for practical applications of protein structure models that need atomic‐detailed resolution such as protein and ligand design. We evaluated the accuracy of eight side‐chain prediction methods in reproducing the side‐chain conformations of experimentally solved structures deposited to the Protein Data Bank. Prediction accuracy was evaluated for a total of four different structural environments (buried, surface, interface, and membrane‐spanning) in three different protein types (monomeric, multimeric, and membrane). Overall, the highest accuracy was observed for buried residues in monomeric and multimeric proteins. Notably, side‐chains at protein interfaces and membrane‐spanning regions were better predicted than surface residues even though the methods did not all use multimeric and membrane proteins for training. Thus, we conclude that the current methods are as practically useful for modeling protein docking interfaces and membrane‐spanning regions as for modeling monomers. Proteins 2014; 82:1971–1984. © 2014 Wiley Periodicals, Inc.     

Effect of Alkylsilyl Side‐Chain Structure on Photovoltaic Properties of Conjugated Polymer Donors

Side‐chain engineering is an important strategy for optimizing photovoltaic properties of organic photovoltaic materials. In this work, the effect of alkylsilyl side‐chain structure on the photovoltaic properties of medium bandgap conjugated polymer donors is studied by synthesizing four new polymers J70 , J72 , J73 , and J74 on the basis of highly efficient polymer donor J71 by changing alkyl substituents of the alkylsilyl side chains of the polymers. And the photovoltaic properties of the five polymers are studied by fabricating polymer solar cells (PSCs) with the polymers as donor and an n‐type organic semiconductor (n‐OS) m‐ITIC as acceptor. It is found that the shorter and linear alkylsilyl side chain could afford ordered molecular packing, stronger absorption coefficient, higher charge carrier mobility, thus results in higher J_sc and fill factor values in the corresponding PSCs. While the polymers with longer or branched alkyl substituents in the trialkylsilyl group show lower‐lying highest occupied molecular orbital energy levels which leads to higher V_oc of the PSCs. The PSCs based on J70 :m‐ITIC and J71 :m‐ITIC achieve power conversion efficiency (PCE) of 11.62 and 12.05%, respectively, which are among the top values of the PSCs reported in the literatures so far.     

Molprobity's ultimate rotamer‐library distributions for model validation

Here we describe the updated MolProbity rotamer‐library distributions derived from an order‐of‐magnitude larger and more stringently quality‐filtered dataset of about 8000 (vs. 500) protein chains, and we explain the resulting changes and improvements to model validation as seen by users. To include only side‐chains with satisfactory justification for their given conformation, we added residue‐specific filters for electron‐density value and model‐to‐density fit. The combined new protocol retains a million residues of data, while cleaning up false‐positive noise in the multi‐ datapoint distributions. It enables unambiguous characterization of conformational clusters nearly 1000‐fold less frequent than the most common ones. We describe examples of local interactions that favor these rare conformations, including the role of authentic covalent bond‐angle deviations in enabling presumably strained side‐chain conformations. Further, along with favored and outlier, an allowed category (0.3–2.0% occurrence in reference data) has been added, analogous to Ramachandran validation categories. The new rotamer distributions are used for current rotamer validation in MolProbity and PHENIX, and for rotamer choice in PHENIX model‐building and refinement. The multi‐dimensional distributions and Top8000 reference dataset are freely available on GitHub. These rotamers are termed “ultimate” because data sampling and quality are now fully adequate for this task, and also because we believe the future of conformational validation should integrate side‐chain with backbone criteria. Proteins 2016; 84:1177–1189. © 2016 Wiley Periodicals, Inc.     

How do side chains orient globally in protein structures?

An angle Omega is defined to serve as a metric for global side-chain orientations, which reflects the orientation of the side chain relative to the radial vector from the center of the protein to an amino acid. The side-chain orientations of buried residues exhibit characteristically different orientations than do exposed residues, in both monomeric and dimeric structures. Overall, buried side chains point mostly inward, whereas surface side chains tend to point outward from the surface. This difference in behavior also correlates well with the residue hydrophobicity; so a global side-chain orientation can be viewed as a direct structural manifestation of hydrophobicity. When various solvent-accessible layers are considered, the behavior is relatively continuous between centrally located and exposed residues. In the case of interfacial residues between subunits, there are statistically significant differences between exposed residues and interface residues for ALA, ARG, ASN, ASP, GLU, HIS, LYS, THR, VAL, MET, PRO, and overall the interface residues have an increased tendency to point inward. Presumably, these substantial differences in orientations of side chains may be a manifestation of hydrophobic forces.     

Comparing side chain packing in soluble proteins,protein‐protein interfaces,and transmembrane proteins

We compare side chain prediction and packing of core and non‐core regions of soluble proteins, protein‐protein interfaces, and transmembrane proteins. We first identified or created comparable databases of high‐resolution crystal structures of these 3 protein classes. We show that the solvent‐inaccessible cores of the 3 classes of proteins are equally densely packed. As a result, the side chains of core residues at protein‐protein interfaces and in the membrane‐exposed regions of transmembrane proteins can be predicted by the hard‐sphere plus stereochemical constraint model with the same high prediction accuracies (>90%) as core residues in soluble proteins. We also find that for all 3 classes of proteins, as one moves away from the solvent‐inaccessible core, the packing fraction decreases as the solvent accessibility increases. However, the side chain predictability remains high (80% within ) up to a relative solvent accessibility, , for all 3 protein classes. Our results show that % of the interface regions in protein complexes are “core”, that is, densely packed with side chain conformations that can be accurately predicted using the hard‐sphere model. We propose packing fraction as a metric that can be used to distinguish real protein‐protein interactions from designed, non‐binding, decoys. Our results also show that cores of membrane proteins are the same as cores of soluble proteins. Thus, the computational methods we are developing for the analysis of the effect of hydrophobic core mutations in soluble proteins will be equally applicable to analyses of mutations in membrane proteins.     

Rat cytochrome P450C24 (CYP24) does not metabolize 1,25-dihydroxyvitamin D2 to calcitroic acid

1alpha-Hydroxy-23 carboxy-24,25,26,27-tetranorvitamin D(3) (calcitroic acid) is known to be the major water-soluble metabolite produced during the deactivation of 1,25-(OH)(2)D(3). This deactivation process is carried out exclusively by the multicatalytic enzyme CYP24 and involves a series of oxidation reactions at C(24) and C(23) leading to side-chain cleavage and, ultimately, formation of the calcitroic acid. Like 1,25-(OH)(2)D(3), 1alpha,25-1,25-(OH)(2)D(2) is also known to undergo side-chain oxidation and side-chain cleavage to form calcitroic acid (Zimmerman et al. [2001]. 1,25-(OH)(2)D(2) differs from 1,25-(OH)(2)D(3) by the presence of a double bond at C(22) and a methyl group at C(24). To date, there have been no studies detailing the participation of CYP24 in the production of calcitroic acid from 1,25-(OH)(2)D(2). We, therefore, studied the metabolism of 1,25-(OH)(2)D(3) and 1,25-(OH)(2)D(2) using a purified rat CYP24 system. Lipid and aqueous-soluble metabolites were prepared for characterization. Aqueous-soluble metabolites were subjected to reverse-phase high-pressure liquid chromatography (HPLC) analysis. As expected, 1,23(OH)(2)-24,25,26,27-tetranor D and calcitroic acid were the major lipid and aqueous-soluble metabolites, respectively, when 1,25-(OH)(2)D(3) was used as substrate. However, when 1,25-(OH)(2)D(2) was used as substrate, 1,24(R),25-(OH)(3)D(2) was the major lipid-soluble metabolite with no evidence for the production of either 1,23(OH)(2)-24,25,26,27-tetranor D or calcitroic acid. Apparently, the CYP24 was able to 24-hydroxylate 1,25-(OH)(2)D(2), but was unable to effect further changes, which would result in side-chain cleavage. These data suggest that the presence of either the double bond at C(22) or the C(24) methyl group impedes the metabolism of 1,25-(OH)(2)D(2) to calcitroic acid by CYP24 and that enzymes other than CYP24 are required to effect this process.     

Protein design simulations suggest that side-chain conformational entropy is not a strong determinant of amino acid environmental preferences

Loss of side-chain conformational entropy is an important force opposing protein folding and the relative preferences of the amino acids for being buried or solvent exposed may be partially determined by which amino acids lose more side-chain entropy when placed in the core of a protein. To investigate these preferences, we have incorporated explicit modeling of side-chain entropy into the protein design algorithm, RosettaDesign. In the standard version of the program, the energy of a particular sequence for a fixed backbone depends only on the lowest energy side-chain conformations that can be identified for that sequence. In the new model, the free energy of a single amino acid sequence is calculated by evaluating the average energy and entropy of an ensemble of structures generated by Monte Carlo sampling of amino acid side-chain conformations. To evaluate the impact of including explicit side-chain entropy, sequences were designed for 110 native protein backbones with and without the entropy model. In general, the differences between the two sets of sequences are modest, with the largest changes being observed for the longer amino acids: methionine and arginine. Overall, the identity between the designed sequences and the native sequences does not increase with the addition of entropy, unlike what is observed when other key terms are added to the model (hydrogen bonding, Lennard-Jones energies, and solvation energies). These results suggest that side-chain conformational entropy has a relatively small role in determining the preferred amino acid at each residue position in a protein.     

Study of electrostatic potential surface distribution of wild-type plastocyanin Synechocystis solution structure determined by homonuclear NMR

Plastocyanin is a small (approximately 10 kDa), type I blue copper protein that works as an electron donor to photosystem I from cytochrome f in both chloroplast systems and in some strains of cyanobacteria. Comparative studies of the kinetic mechanisms of plastocyanins in different organisms show that the electron transfer from photosystem I happens by simple collision in cyanobacteria but through a intermediate transition complex in green algae and superior plants. Previous work has proved that this effect cannot be explained by structural variations across the different plastocyanins but it can be explained by differences in the electrostatic potential distribution at the protein surface. In that case, minor conformational errors at the amino acid side chain level may imply an important effect in the electrostatic potential distribution calculation. In this work we present a high resolution study of side chain conformation by homonuclear NMR for the reduced wild-type plastocyanin Synechocystis using intensity ratios for 2D-NOESY and 2D-H,H-TOCSY cross peaks at different mixing times. We also present the corresponding comparison with different plastocyanin structures and the effect in the electrostatic potential distribution at the protein surface. We discuss the importance of indirect J-coupling information from TOCSY-type experiments as complement for intraresidue distances derived from NOESY experiments in the determination of side chain orientation and stereo-specific assignments.     

Computational protein design with side-chain conformational entropy

Recent advances in modeling protein structures at the atomic level have made it possible to tackle "de novo" computational protein design. Most procedures are based on combinatorial optimization using a scoring function that estimates the folding free energy of a protein sequence on a given main-chain structure. However, the computation of the conformational entropy in the folded state is generally an intractable problem, and its contribution to the free energy is not properly evaluated. In this article, we propose a new automated protein design methodology that incorporates such conformational entropy based on statistical mechanics principles. We define the free energy of a protein sequence by the corresponding partition function over rotamer states. The free energy is written in variational form in a pairwise approximation and minimized using the Belief Propagation algorithm. In this way, a free energy is associated to each amino acid sequence: we use this insight to rescore the results obtained with a standard minimization method, with the energy as the cost function. Then, we set up a design method that directly uses the free energy as a cost function in combination with a stochastic search in the sequence space. We validate the methods on the design of three superficial sites of a small SH3 domain, and then apply them to the complete redesign of 27 proteins. Our results indicate that accounting for entropic contribution in the score function affects the outcome in a highly nontrivial way, and might improve current computational design techniques based on protein stability.     

A consistent set of statistical potentials for quantifying local side-chain and backbone interactions

The frequencies of occurrence of atom arrangements in high-resolution protein structures provide some of the most accurate quantitative measures of interaction energies in proteins. In this report we extend our development of a consistent set of statistical potentials for quantifying local interactions between side-chains and the polypeptide backbone, as well as nearby side-chains. Starting with phi/psi/chi1 propensities that select for optimal interactions of the 20 amino acid side-chains with the 2 flanking peptide bonds, the following 3 new terms are added: (1) a distance-dependent interaction between the side-chain at i and the carbonyl oxygens and amide protons of the peptide units at i +/- 2, i +/- 3, and i +/- 4; (2) a distance-dependent interaction between the side-chain at position i and side-chains at positions i + 1 through i + 4; and (3) an orientation-dependent interaction between the side-chain at position i and side-chains at i + 1 through i + 4. The relative strengths of these 4 pseudo free energy terms are estimated by the average information content of each scoring matrix and by assessing their performance in a simple fragment threading test. They vary from -0.4 - -0.5 kcal/mole per residue for phi/psi/chi1 propensities to a range of -0.15 - -0.6 kcal/mole per residue for each of the other 3 terms. The combined energy function, containing no interactions between atoms more than 4 residues apart, identifies the correct structural fragment for randomly selected 15 mers over 40% of the time, after searching through 232,000 alternative conformations. For 14 out of 20 sets of all-atom Rosetta decoys analyzed, the native structure has a combined score lower than any of the 1700-1900 decoy conformations. The ability of this energy function to detect energetically important details of local structure is demonstrated by its power to distinguish high-resolution crystal structures from NMR solution structures.     

Side‐Chain Engineering for Fine‐Tuning of Energy Levels and Nanoscale Morphology in Polymer Solar Cells

A series of four polymers containing benzo[1,2‐b:4,5‐b′]dithiophene (BDT) and 5,6‐difluoro‐4,7‐diiodobenzo[c][1,2,5]thiadiazole (2FBT), PBDT2FBT, PBDT2FBT‐O, PBDT2FBT‐T, and PBDT2FBT‐T‐O, are synthesized with their four different side chains, alkyl‐, alkoxy‐, alkylthienyl‐, and alkoxythienyl. Experimental results and theoretical calculations show that the molecular tuning of the side chains simultaneously influences the solubilities, energy levels, light absorption, surface tension, and intermolecular packing of the resulting polymers by altering their molecular coplanarity and electron affinity. The polymer solar cell (PSC) based on a blend of PBDT2FBT‐T/[6,6]‐phenyl‐C₇₁‐butyric acid methyl ester (PC₇₁BM) exhibits the best photovoltaic performance of the four PBDT2FBT derivatives, with a high open‐circuit voltage of 0.98 V and a power conversion efficiency of 6.37%, without any processing additives, post‐treatments, or optical spacers. Furthermore, PBDT2FBT‐T‐O, which has a novel side chain alkoxythienyl, showed promising properties with the most red‐shifted absorption and strong intermolecular packing property in solid state. This study provides insight into molecular design and fabrication strategies via structural tuning of the side chains of conjugated polymers for achieving highly efficient PSCs.     

Dinosterol side chain biosynthesis in a marine dinoflagellate, Crypthecodinium cohnii

The heterotrophic dinofiagellate, Crypthecodinium cohnii, cultured in a nutrient medium containing methionine-[CD₃] incorporated deuterium into the newly synthesized 4α-monomethyl compound dinosterol (4α,23,24-trimethylcholest-22-en-3β-ol). The MS fragmentation pattern indicated that the C-23 methyl group contained three deuterium atoms and was introduced intact by transmethylation from methionine. The C-24 methyl group contained only two deuterium atoms which is consistent with the production of a 24-methylenesterol intermediate which is subsequently reduced to give the 24-methyl side chain. Mechanisms are proposed to account for the production of the dinosterol side chain.