Fast folding dynamics of an α-helical peptide with bulky side chains

2004 ◽  
Vol 6 (5) ◽  
pp. 1022-1030 ◽  
Author(s):  
Sarah A. Petty ◽  
Martin Volk
Keyword(s):  
Side Chains ◽  
Helical Peptide ◽  
Folding Dynamics

scholarly journals Trajectory-Based Parameterization of a Coarse-Grained Forcefield for High-Thoughput Protein Simulation

2017 ◽  
Author(s):  
John M. Jumper ◽  
Karl F. Freed ◽  
Tobin R. Sosnick
Keyword(s):  
Computational Efficiency ◽  
De Novo ◽  
Coarse Grained ◽  
Side Chains ◽  
Time Step ◽  
Trade Off ◽  
Protein Simulation ◽  
Starting Point ◽  
Folding Dynamics ◽  
Contrastive Divergence

The traditional trade-off in biomolecular simulation between accuracy and computational efficiency is predicated on the assumption that detailed forcefields are typically well-parameterized (i.e. obtaining a significant fraction of possible accuracy). We re-examine this trade-off in the more realistic regime in which parameterization is a greater source of bias than the level of detail in the forcefield. To address parameterization of coarse-grained forcefields, we use the contrastive divergence technique from machine learning to train directly from simulation trajectories on 450 proteins. In our scheme, the computational efficiency of the model enables high accuracy through precise tuning of the Boltzmann ensemble over a large collection of proteins. This method is applied to our recently developed Upside model [1], where the free energy for side chains are rapidly calculated at every time-step, allowing for a smooth energy landscape without steric rattling of the side chains. After our contrastive divergence training, the model is able to fold proteins up to approximately 100 residues de novo on a single core in CPU core-days. Additionally, the improved Upside model is a strong starting point both for investigation of folding dynamics and as an inexpensive Bayesian prior for protein physics that can be integrated with additional experimental or bioinformatic data.

Influence of Flexible Side-Chains on the Breathing Phase Transition of Pillared Layer MOFs: A Force Field Investigation

2020 ◽  
Author(s):  
Julian Keupp ◽  
Johannes P. Dürholt ◽  
Rochus Schmid
Keyword(s):  
First Principles ◽  
Good Accuracy ◽  
Field Investigation ◽  
Square Lattice ◽  
Side Chain ◽  
Second Step ◽  
Side Chains ◽  
Dynamics Simulations ◽  
Complex Phenomena ◽  
Closed Pore

The prototypical pillared layer MOFs, formed by a square lattice of paddle-<br>wheel units and connected by dinitrogen pillars, can undergo a breathing phase<br>transition by a “wine-rack” type motion of the square lattice. We studied this not<br>yet fully understood behavior using an accurate first principles parameterized force<br>field (MOF-FF) for larger nanocrystallites on the example of Zn 2 (bdc) 2 (dabco) [bdc:<br>benzenedicarboxylate, dabco: (1,4-diazabicyclo[2.2.2]octane)] and found clear indi-<br>cations for an interface between a closed and an open pore phase traveling through<br>the system during the phase transformation [Adv. Theory Simul. 2019, 2, 11]. In<br>conventional simulations in small supercells this mechanism is prevented by periodic<br>boundary conditions (PBC), enforcing a synchronous transformation of the entire<br>crystal. Here, we extend this investigation to pillared layer MOFs with flexible<br>side-chains, attached to the linker. Such functionalized (fu-)MOFs are experimen-<br>tally known to have different properties with the side-chains acting as fixed guest<br>molecules. First, in order to extend the parameterization for such flexible groups,<br>1a new parametrization strategy for MOF-FF had to be developed, using a multi-<br>structure force based fit method. The resulting parametrization for a library of<br>fu-MOFs is then validated with respect to a set of reference systems and shows very<br>good accuracy. In the second step, a series of fu-MOFs with increasing side-chain<br>length is studied with respect to the influence of the side-chains on the breathing<br>behavior. For small supercells in PBC a systematic trend of the closed pore volume<br>with the chain length is observed. However, for a nanocrystallite model a distinct<br>interface between a closed and an open pore phase is visible only for the short chain<br>length, whereas for longer chains the interface broadens and a nearly concerted trans-<br>formation is observed. Only by molecular dynamics simulations using accurate force<br>fields such complex phenomena can be studied on a molecular level.

Pathway Complexity in the Stacking of Imine-linked Macrocycles Related to Two-Dimensional Covalent Organic Frameworks

2019 ◽  
Author(s):  
Shiwei Wang ◽  
Anton Chavez ◽  
Simil Thomas ◽  
Hong Li ◽  
Nathan C. Flanders ◽  
...  
Keyword(s):  
Temperature Dependence ◽  
Structural Similarity ◽  
Discrete Models ◽  
Side Chains ◽  
Two Dimensional ◽  
Assembly Process ◽  
Covalent Organic Frameworks ◽  
Electron Systems ◽  
Monomer Structure ◽  
Kinetic Traps

This work reports on the assembly of imine-linked macrocycles that serve as models of two-dimensional covalent organic frameworks (2D COFs). Interlayer interactions play an important role in the formation of 2D COFs, yet the effect of monomer structure on COF formation, crystallinity, and susceptibility to exfoliation are not well understood. For example, monomers with both electron-rich and electron-poor π-electron systems have been proposed to strengthen interlayer inter-actions and improve crystallinity. Here we probe these effects by studying the stacking behavior of imine-linked macrocycles that represent discrete models of 2D COFs. <div><br></div><div>Specifically, macrocycles based on terephthaldehyde (PDA) or 2,5-dimethoxyterephthaldehyde (DMPDA) stack upon cooling molecularly dissolved solutions. Both macrocycles assemble cooperatively with similar ΔHe values of -97 kJ/mol and -101 kJ/mol, respectively, although the DMPDA macrocycle assembly process showed a more straightforward temperature dependence. Circular dichroism spectroscopy performed on macrocycles bearing chiral side chains revealed a helix reversion process for the PDA macrocycles that was not observed for the DMPDA macrocycles. <br></div><div><br></div><div>Given the structural similarity of these monomers, these findings demonstrate that the stacking processes associated with nanotubes derived from these macrocycles, as well as for the corresponding COFs, are complex and susceptible to kinetic traps, casting doubt on the relevance of thermodynamic arguments for improving materials quality. <br></div>

Predicting the Strength of Stacking Interactions Between Heterocycles and Aromatic Amino Acid Side Chains

2019 ◽  
Author(s):  
Andrea N. Bootsma ◽  
Analise C. Doney ◽  
Steven Wheeler
Keyword(s):  
Amino Acid ◽  
Binding Sites ◽  
Aromatic Amino Acid ◽  
Aromatic Amino Acids ◽  
Biologically Active ◽  
Side Chains ◽  
Stacking Interactions ◽  
Inhibitor Binding ◽  
Protein Binding Sites ◽  
Amino Acid Side Chains

<p>Despite the ubiquity of stacking interactions between heterocycles and aromatic amino acids in biological systems, our ability to predict their strength, even qualitatively, is limited. Based on rigorous <i>ab initio</i> data, we have devised a simple predictive model of the strength of stacking interactions between heterocycles commonly found in biologically active molecules and the amino acid side chains Phe, Tyr, and Trp. This model provides rapid predictions of the stacking ability of a given heterocycle based on readily-computed heterocycle descriptors. We show that the values of these descriptors, and therefore the strength of stacking interactions with aromatic amino acid side chains, follow simple predictable trends and can be modulated by changing the number and distribution of heteroatoms within the heterocycle. This provides a simple conceptual model for understanding stacking interactions in protein binding sites and optimizing inhibitor binding in drug design.</p>

A Strategy for Thioamide Incorporation During Fmoc Solid-Phase Peptide Synthesis with Robust Stereochemical Integrity

2019 ◽  
Author(s):  
luis camacho III ◽  
Bryan J. Lampkin ◽  
Brett VanVeller
Keyword(s):  
Amino Acid ◽  
Functional Groups ◽  
Peptide Synthesis ◽  
Solid Phase ◽  
Solid Phase Peptide Synthesis ◽  
Side Chains ◽  
Amino Acid Side Chains ◽  
Peptide Elongation

We describe a method to protect the sensitive stereochemistry of the thioamide—in analogy to the protection of the functional groups of amino acid side chains—in order to preserve the thioamide moiety during peptide elongation.<br>

The Total Synthesis of Rhabdastrellic Acid A

2018 ◽  
Author(s):  
Yaroslav Boyko ◽  
Christopher Huck ◽  
David Sarlah
Keyword(s):  
Total Synthesis ◽  
Late Stage ◽  
Cross Coupling ◽  
Side Chains ◽  
General Strategy ◽  
Modular Approach ◽  
Linear Sequence ◽  
Generating Sequence ◽  
First Time

<div>The first total synthesis of rhabdastrellic acid A, a highly cytotoxic isomalabaricane triterpenoid, has been accomplished in a linear sequence of 14 steps from commercial geranylacetone. The prominently strained <i>trans-syn-trans</i>-perhydrobenz[<i>e</i>]indene core characteristic of the isomalabaricanes is efficiently accessed in a selective manner for the first time through a rapid, complexity-generating sequence incorporating a reductive radical polyene cyclization, an unprecedented oxidative Rautenstrauch cycloisomerization, and umpolung 𝛼-substitution of a <i>p</i>-toluenesulfonylhydrazone with in situ reductive transposition. A late-stage cross-coupling in concert with a modular approach to polyunsaturated side chains renders this a general strategy for the synthesis of numerous family members of these synthetically challenging and hitherto inaccessible marine triterpenoids.</div>

Thioether-Facilitated Iridium-Catalyzed Hydrosilylation of Steric 1,1-Disubstituted Olefins

2019 ◽  
Author(s):  
Shengtao Ding
Keyword(s):  
Side Chains ◽  
Feasible Method ◽  
Iridium Catalysis ◽  
Efficient Strategy ◽  
Terminal Alkenes ◽  
And Control ◽  
Sulfur Containing ◽  
Organosilicon Polymers

<p>One facile and efficient strategy for the hydrosilylation of steric 1,1-disubstituted terminal alkenes is demonstrated. Investigations on substrate scope and control experiments revealed the necessity of thioether in promoting this process under a simple iridium catalysis system. This convenient and feasible method is expected to be useful in the synthesis of sulfur-containing organosilicon polymers with different side-chains.</p><p><br></p>

Polysaccharide Structures in the Outer Mucilage of Arabidopsis Seeds Visualized by AFM

2020 ◽  
Author(s):  
MAK Williams ◽  
V Cornuault ◽  
AH Irani ◽  
VV Symonds ◽  
J Malmström ◽  
...  
Keyword(s):  
Average Length ◽  
American Chemical Society ◽  
Md Simulations ◽  
Chemical Society ◽  
Side Chains ◽  
Rhamnogalacturonan I ◽  
Afm Imaging ◽  
Minor Population ◽  
The Stability ◽  
A Minor

© 2020 American Chemical Society. Evidence is presented that the polysaccharide rhamnogalacturonan I (RGI) can be biosynthesized in remarkably organized branched configurations and surprisingly long versions and can self-assemble into a plethora of structures. AFM imaging has been applied to study the outer mucilage obtained from wild-type (WT) and mutant (bxl1-3 and cesa5-1) Arabidopsis thaliana seeds. For WT mucilage, ordered, multichain structures of the polysaccharide RGI were observed, with a helical twist visible in favorable circumstances. Molecular dynamics (MD) simulations demonstrated the stability of several possible multichain complexes and the possibility of twisted fibril formation. For bxl1-3 seeds, the imaged polymers clearly showed the presence of side chains. These were surprisingly regular and well organized with an average length of ∼100 nm and a spacing of ∼50 nm. The heights of the side chains imaged were suggestive of single polysaccharide chains, while the backbone was on average 4 times this height and showed regular height variations along its length consistent with models of multichain fibrils examined in MD. Finally, in mucilage extracts from cesa5-1 seeds, a minor population of chains in excess of 30 μm long was observed.

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