CarbBuilder: Software for building molecular models of complex oligo‐ and polysaccharide structures

Kuttel, Michelle M.; Ståhle, Jonas; Widmalm, Göran

doi:10.1002/jcc.24428

Cited by 75 publications

(65 citation statements)

References 24 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“… Molecular model of the 20‐mer maltoicosaose generated by CarbBuilder with torsion angle ϕ =−18° and ψ =−19° (see above) and subsequently geometry‐optimized using tight binding density functional theory DFTB3 and a polarizable continuum model (PCM) representing water as solvent.…”

Section: Resultsmentioning

confidence: 99%

“…The system was then simulated in the NPT ensemble and trajectory data were collected for 50 ns or 100 ns. The maltoicosaose structure was built using CarbBuilder and geometry optimized with DFTB3 using the PCM implicit solvent model set as implemented in GAMESS‐US software package …”

Section: Methodsmentioning

confidence: 99%

“…[40] Amylosed issolved in dimethyl sulfoxide is a tight helix but with an increased water content the intramolecular hydrogen bonding decreases and transitionf rom ah elix to al oose helix to ar andom coil occurs, as deduced by spectroscopic methods including 13 CNMR chemical shift data. [83] Based on the MD simulations presented herein am olecular model of the 20-mer maltoicosaose generated by molecular modeling using CarbBuilder [84] startingf rom an O2'···HO3accessible hydrogen-bond arrangement and subsequent DFTbased geometry optimization resulted in al eft-handed helical structure ( Figure 9).…”

Section: Maltose and Amylosementioning

confidence: 99%

“…[97] Stan- Figure 9. Molecular model of the 20-mer maltoicosaose generated by Carb-Builder [84] with torsion angle f = À188 and y = À198 (seeabove) andsubsequently geometry-optimized using tight bindingd ensity functional theory DFTB3 and apolarizable continuum model (PCM) representing watera ss olvent. dard workup, silica-based purification, and hydrogenolysis followed by gel-permeation chromatography resulted in disaccharide 4,t he 1 Ha nd 13 CNMR data of which are given in Ta ble 1.…”

Section: Synthesismentioning

confidence: 99%

“…The system was then simulated in the NPT ensemble and trajectory data were collected for 50 ns or 100 ns. The maltoicosaose structure was built using CarbBuilder [84] and geometry optimized with DFTB3 [114] using the PCM implicit solvent model set as implemented in GAMESS-US software package. [115,116] Calculation of three-bond spin-spin coupling constants from the MD simulations utilized Equations (1), (2), and (3): [55,57,58]…”

Section: Synthesismentioning

confidence: 99%

See 4 more Smart Citations

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

et al. 2019

Self Cite

View full text Add to dashboard Cite

Carbohydrates, also known as glycans in biological systems, are omnipresent in nature where they as glycoconjugates occur as oligo‐ and polysaccharides linked to lipids and proteins. Their three‐dimensional structure is defined by two or three torsion angles at each glycosidic linkage. In addition, transglycosidic hydrogen bonding between sugar residues may be important. Herein we investigate the presence of these inter‐residue interactions by NMR spectroscopy in D2O/[D6]DMSO (70:30) or D2O and by molecular dynamics (MD) simulations with explicit water as solvent for disaccharides with structural elements α‐d‐Manp‐(1→2)‐d‐Manp, β‐d‐GlcpNAc‐(1→2)‐d‐Manp, and α‐d‐Glcp‐(1→4)‐β‐d‐Glcp, all of which have been suggested to exhibit inter‐residue hydrogen bonding. For the disaccharide β‐d‐GlcpNAc‐(1→2)‐β‐d‐Manp‐OMe, the large extent of O5′⋅⋅⋅HO3 hydrogen bonding as seen from the MD simulation is implicitly supported by the 1H NMR chemical shift and 3JHO3,H3 value of the hydroxy proton. In the case of α‐d‐Glcp‐(1→4)‐β‐d‐Glcp‐OMe, the existence of a transglycosidic hydrogen bond O2′⋅⋅⋅HO3 was proven by the presence of a cross‐peak in 1H,13C HSQC‐TOCSY experiments as a result of direct TOCSY transfer between HO3 of the reducing end residue and H2′ (detected at C2′) of the terminal residue. The occurrence of inter‐residue hydrogen bonding, albeit transient, is judged important for the stabilization of three‐dimensional structures, which may be essential in maintaining a conformational state for carbohydrate–protein interactions of glycans to take place in biologically important environments.

show abstract

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Maltose and Amylosementioning

confidence: 99%

Section: Synthesismentioning

confidence: 99%

Section: Synthesismentioning

confidence: 99%

See 3 more Smart Citations

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

et al. 2019

Self Cite

View full text Add to dashboard Cite

show abstract

Glycogen as a Building Block for Advanced Biological Materials

2019

View full text Add to dashboard Cite

complex drug delivery systems that are challenging to scale up and therefore have limited clinical and commercial translation. Although numerous nanoparticles have been widely developed and used for various applications, including biomedical applications, [2] there is a growing interest in nontoxic and degradable alternatives to first-generation synthetic nanomaterials. Ideally the synthesis of such nanoparticles needs to be cost effective, simple, green, reproducible, scalable, and the constitutive building blocks of the nanoparticles should be nontoxic, functional, biodegradable, and available on a large scale. Naturally occurring nanoparticles could be such a valid alternative. These nanoparticles include intracellular structures, such as magnetosomes [3] and glycogen, and extracellular assemblies such as lipoproteins and viruses. [3] Among these, glycogen is the most abundant and versatile biological nanoparticle, which fulfils the requirements for the fabrication of nanostructured biomaterials. Glycogen is nature's prime nanoparticle that exists in most organisms, from bacteria and archaea to humans, [4,5] as a vital component of the cellular energy machinery. It is a highly branched polysaccharide comprising repeating units of glucose connected by linear α-d-(1,4) glycosidic linkages with α-d-(1,6) branching, structured into roughly spherical nanoparticles that have a high water solubility and molecular weight.The use of polysaccharides as components for advanced materials has been an attractive concept for decades. [6,7] A key motive is that polysaccharides, as a natural biomaterial, are endowed with a level of biodegradability and biocompatibility. In addition, they can be easily modified chemically or biochemically to produce functional derivatives, which are important for various therapeutic applications. [8] The structures of polysaccharides vary considerably but span from linear to highly branched polymers with molecular weights ranging from thousands to millions, composed of mono-or disaccharides, or short-chain oligomers bound together by glycosidic linkages. [9] There is a rich history of research on the use of polysaccharides in a range of therapeutic applications including: i) soft tissue engineering, [10,11] where the materials can be designed to mimic the mechanical properties of the extracellular matrix in the tissue; ii) as drug, protein, or gene delivery systems, [7,12,13] where polysaccharides have a large number of reactive groups [14] that allow for tunable properties [12] such as pH-responsiveness; [15] and iii) as nanoprobes for cellular Biological nanoparticles found in living systems possess distinct molecular architectures and diverse functions. Glycogen is a unique biological polysaccharide nanoparticle fabricated by nature through a bottom-up approach. The biocatalytic synthesis of glycogen has evolved over time to form a nanometer-sized dendrimer-like structure (20-150 nm) with a highly branched surface and a dense core. This makes glycogen markedly different from other natur...

show abstract

prepareforleap: An automated tool for fast PDB‐to‐parameter generation

Roe

Bergonzo

2022

J Comput Chem

View full text Add to dashboard Cite

Setting up molecular dynamics simulations from experimentally determined structures is often complicated by a variety of factors, particularly the inclusion of carbohydrates, since these have several anomer types which can be linked in a variety of ways. Here we present a stand‐alone tool implemented in the widely‐used software CPPTRAJ that can be used to automate building structures and generating a “ready to run” parameter and coordinate file pair. This tool automatically identifies carbohydrate anomer type, configuration, linkage, and functional groups, and performs topology modifications (e.g., renaming residue/atom names) required to build the final system using state of the art GLYCAM force field parameters. It will also generate the necessary commands for bonding carbohydrates and creating any disulfide bonds.

show abstract

CarbBuilder: Software for building molecular models of complex oligo‐ and polysaccharide structures

Cited by 75 publications

References 24 publications

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

Inter‐residual Hydrogen Bonding in Carbohydrates Unraveled by NMR Spectroscopy and Molecular Dynamics Simulations

Glycogen as a Building Block for Advanced Biological Materials

prepareforleap: An automated tool for fast PDB‐to‐parameter generation

Contact Info

Product

Resources

About