LTR review dataset

LTR article coding datase

Effect of Carbon Spacer Length on Zwitterionic Carboxybetaines

Zwitterionic carboxybetaines (CBs) are ubiquitous in nature and considered promising materials for biological and chemical applications. A thorough understanding of the effect of carbon spacer length (CSL) on molecular properties is important. In this work, using molecular dynamics simulation and quantum chemical calculation, we investigated the effect of CSL on the molecular properties of CB molecules. The hydration number, structure, and dynamics of carboxylic and trimethyl ammonium groups were investigated and found to present different behaviors in regards to the variation of CSL. The simulation results with partial charges developed from quantum chemical calculations were compared with those with partial charges from the OPLS all atom (OPLSAA) force field. The hydration free energy of CB molecules and CB–Na+ association was also studied as a function of CSL

Influence of Charged Groups on the Properties of Zwitterionic Moieties: A Molecular Simulation Study

Zwitterionic carboxybetaine and sulfobetaine materials have shown an excellent ability to resist nonspecific protein adsorption. It is desirable to obtain a better understanding of zwitter­ionic materials based on their molecular structures. This work aims to understand the roles of charged groups in zwitter­ionic moieties and to design new protein-resistant zwitter­ionic moieties beyond carboxy­betaine and sulfo­betaine. We conducted molecular simulations to study the hydration, self-association, and protein interactions of 12 zwitter­ionic moieties derived from three anionic groups (carboxylic, sulfonate, and sulfate) and four cationic groups (quaternary ammonium, tertiary ammonium, secondary ammonium, and primary ammonium). The partial charges of atoms in these moieties were obtained from quantum chemical calculations. Hydration was studied by evaluating the hydration free energy of moieties and the hydration structure and dynamics of the charged groups. All zwitter­ionic moieties have strong hydration, but their structural and dynamic properties depend on the types of cationic and anionic groups involved. The self-association and protein interactions of zwitter­ionic moieties also show relationships with the charged groups. Our simulation results indicate good protein-resistant ability of several zwitter­ionic moieties, one of which has also been shown by recent experiments

Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study

A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids’ nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures

Molecular Dynamics Simulation Study of Ion Interactions with Zwitterions

Using molecular dynamics simulations, we investigated the associations between two zwitterions (carboxybetaine and sulfobetaine) and four types of cations (Li+, Na+, K+, and Cs+) in aqueous solutions. We studied the number and lifetime of various zwitterion–cation associations and observed that both carboxybetaine and sulfobetaine have the same order of association number and lifetime: Li+ > Na+ > K+ > Cs+. Simulation results showed that the association variation as a function of cation types for these two zwitterions is significantly different. The effect of anion type on the order was also investigated by varying the type of anions from Cl– to Br– and F–. In order to further investigate zwitterion–cation association, we simulated the systems either with one type of zwitterion and two types of cations or with one type of cation and both carboxybetaine and sulfobetaine presented. This allowed direct competition between the solutes, and the observed association number and lifetime validated the order. Simulation results further demonstrated that, although CB associates stronger with Li+ and Na+ than SB, the latter is associated preferentially by K+ and Cs+

Effect of sequence pattern on conformation of DOPA-Peptide conjugate aggregates: a discontinuous molecular dynamics simulation study

Underwater adhesives are critical for many applications, including marine coatings, sealants, and medical devices. Research on natural underwater adhesives has shown that L-3,4-dihydroxyphenylalanine (DOPA) and amyloid nanostructures are vital to their adhesive abilities. The fusion of DOPA-containing chains and amyloid-forming peptides creates a new space for designing underwater adhesives capable of multi-surface adhesion. One critical question for this design is the interplay between the DOPA and amyloid-forming peptide regions. Here we investigate the effect of the sequence pattern of DOPA-containing chains on the aggregation conformation of conjugates. Discontinuous molecular dynamics simulations were performed for fourteen DOPA-amyloid conjugates with different sequence patterns along the DOPA-containing portion. The amyloid-forming portion is represented by KLVFFAE from the Aβ42 peptide. The structural properties of the DOPA-amyloid conjugates are characterised by the percentages of ordered secondary structures and residue-residue contact maps. The results showed that certain patterns of DOPA and glycine in the DOPA-containing tail allowed the KLVFFAE portions of the conjugates to form distinct ordered β-sheets, and the DOPA-containing portion and the KLVFFAE portion of the conjugates to remain separated both within the same chain and amongst different chains. Among the designs, the most promising sequences are KLVFFAE-G-YYGYYGYY (where Y represents DOPA) and KLVFFAE-G-YYYYGGGG.</p

Difference of Carboxybetaine and Oligo(ethylene glycol) Moieties in Altering Hydrophobic Interactions: A Molecular Simulation Study

Polycarboxybetaine and poly­(ethylene glycol) materials resist nonspecific protein adsorption but differ in influencing biological functions such as enzymatic activity. To investigate this difference, we studied the influence of carboxybetaine and oligo­(ethylene glycol) moieties on hydrophobic interactions using molecular simulations. We employed a model system composed of two non-polar plates and studied the potential of mean force of plate–plate association in carboxybetaine, (ethylene glycol)₄, and (ethylene glycol)₂ solutions using well-tempered metadynamics simulations. Water, trimethylamine <i>N</i>-oxide, and urea solutions were used as reference systems. We analyzed the variation of the potential of mean force in various solutions to study how carboxybetaine and oligo­(ethylene glycol) moieties influence the hydrophobic interactions. To study the origin of their influence, we analyzed the normalized distributions of moieties and water molecules using molecular dynamics simulations. The simulation results showed that oligo­(ethylene glycol) moieties repel water molecules away from the non-polar plates and weaken the hydrophobic interactions. Carboxybetaine moieties do not repel water molecules away from the plates and therefore do not influence the hydrophobic interactions

Water Mobility: A Bridge between the Hofmeister Series of Ions and the Friction of Zwitterionic Surfaces in Aqueous Environments

In this work, we systematically studied the effects of monovalent ions in the Hofmeister series on the friction of zwitterionic surfaces with carboxybetaine self-assembled monolayers (CB-SAMs) as model surfaces using molecular dynamics simulations. The friction coefficients between two CB-SAM surfaces under shear were calculated in the presence of LiCl, NaCl, KCl, CsCl, CsF, CsBr, or CsI solutions at 1 M. Results show that there is a strong correlation between the order of ions in the Hofmeister series and the friction of the CB-SAM surfaces. For salt solutions with the same anion, the friction of the surfaces in a solution with kosmotropic cations has larger friction than that in a solution with chaotropic ones. The same relationship between the order of ions in the Hofmeister series and the friction of the surfaces can be found for the salt solutions with the same cation but different anions. The analysis of water near the surfaces further suggests that these surfaces are hydrated with a similar amount of water molecules and the mobility of interfacial water is the key factor that bridges the relationship between the order of ions in the Hofmeister series and the friction of zwitterionic surfaces. High water mobility promotes the lubrication of zwitterionic surfaces

Physiological Levels of Salt and Polyamines Favor Writhe and Limit Twist in DNA

Quantitative analysis of single molecule experiments show that adding either of two natural polyamines, spermine or spermidine, produced more compact plectonemes in DNA in physiological concentrations of monovalent salt. They also promoted plectoneme formation at lower values of torsion in measurements of extension versus twist. Quantifying changes in the plectonemic DNA using some results from simple rod models suggested that exposure to polyamines reduced the radii and increased the densities of plectonemes. Thus, polyamines may limit the twist density by favoring writhe which maintains the B-form. Although polymerases may significantly stretch the double helix, denature DNA, and produce twist instead of writhe, natural polyamines stabilize base-pairing, limit twist to maintain the B-form, and promote supercoiling, which is conducive to replication and transcription and essential for DNA packaging