Volume, Surface and Hydration Properties of Proteins

Durchschlag, Helmut; Zipper, Peter

doi:10.1007/2882_2008_081

Cited by 3 publications

(7 citation statements)

References 17 publications

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“…In PDB2AT, atoms or atomic groups in sequential order are merged into a single bead until their total volume equals or just exceeds that of a bead with arbitrarily chosen bead diameter (BD). Calculation of volumes are based on Traube's additivity principle, summing up volume increments for the basic atoms [15,18,21]. The resulting bead, having a volume, mass, and weight identical to the summed up contributions of the merged atoms or groups, is placed at the local center of gravity of the ensemble of atoms or groups it replaces; usually the radius r b of this bead is slightly larger than BD/2.…”

Section: Methodsmentioning

confidence: 99%

“…While in the past, the comparison of calculated and experimental data of quite different proteins has established the universal validity of the approaches applied (e.g., [6,[9][10][11][12][13][14][15][16][17][18]), a systematic investigation of the reduction approaches including inherent limitations is missing to date. To test the accuracy of the reduction procedures applied, only the structures of models have to be considered to avoid being influenced by a serendipitous coincidence of predicted and observed quantities.…”

Section: Introductionmentioning

confidence: 99%

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Modeling Complex Biological Macromolecules: Reduction of Multibead Models

Zipper

Durchschlag

2007

J Biol Phys

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The shape of simple and complex biological macromolecules can be approximated by bead modeling procedures. Such approaches are required, for example, for the analysis of the scattering and hydrodynamic behavior of the models under analysis and the prediction of their molecular properties. Using the atomic coordinates of proteins for modeling inevitably leads to models composed of a multitude of beads. In particular, for hydrodynamic modeling, a drastic reduction of the bead number may become unavoidable to enable computation. A systematic investigation of different approaches and computation modes shows that the 'running mean', 'cubic grid,' and 'hexagonal grid' approaches are successful, provided that the extent of reduction does not exceed a factor of 100 and the grid approaches use beads of unequal size and the beads are located at the centers of gravity. Further precautions to be taken include usage of appropriate interaction tensors for overlapping beads of unequal size and appropriate volume corrections when calculating intrinsic viscosities. The applied procedures were tested with the small protein lysozyme in a case study and were then applied to the huge capsid of the phage fr and its trimeric building block. The appearance of the models and the agreement of molecular properties and distance distribution functions of unreduced and reduced models can be used as evaluation criteria.

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Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Modeling Complex Biological Macromolecules: Reduction of Multibead Models

Zipper

Durchschlag

2007

J Biol Phys

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“…The molecular volumes thus obtained are either anhydrous volumes or, because of scarce waters, poorly hydrated volumes (Durchschlag & Zipper, 2008). Surface characteristics of proteins are obtained by using analytical surface calculation programs such as SIMS based on the rolling-ball strategy (Vorobjev & Hermans, 1997), yielding molecular surface and solvent-accessible surface areas (i.e.…”

Section: Calculation Of Volumes and Surfacesmentioning

confidence: 99%

“…anhydrous and hydrated surfaces), in addition to a smooth 'molecular dot surface' required for values for the solvent-excluded volume and appliance of advanced hydration modelling strategies. The program SIMS may be applied either to the atomic coordinates or newly-created coordinates (e.g., gravity centres of AA residues) (Durchschlag & Zipper, 2008).…”

Section: Calculation Of Volumes and Surfacesmentioning

confidence: 99%

“…Biophysically relevant hydration details are mandatorily required in certain cases: understanding protein interactions as precondition for flexibility, dynamics and functionality (Creighton, 2010a(Creighton, , 2010bSerdyuk et al, 2007); very precise comparisons of high-resolution 3D structures and molecular parameters with data from solution techniques Durchschlag & Zipper, 2008;Zipper & Durchschlag, 2010b); gaining insight into radiation damage events ; construction of tailor-made nano-compounds in context with drug-design projects and the development of functionalized surfaces and polymers by mimicking proteins (Durchschlag & Zipper, 2008); improvement/check of crystallographic/NMR data with regard to hydration waters .…”

Section: Introductionmentioning

confidence: 99%

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Anhydrous and Hydrated Protein Models Derived from High-Resolution and Low-Resolution Techniques

Durchschlag¹,

Zipper²

2012

Protein Structure

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Photothermal Imaging and Measurement of Protein Shell Stoichiometry of Single HIV-1 Gag Virus-like Nanoparticles

et al. 2011

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Virus life stages often constitute a complex chain of events, difficult to track in-vivo and in real-time. Challenges are associated with spatial and time limitations of current probes: most viruses are smaller than the diffraction limit of optical microscopes while the entire time-scale of virus dynamics spans over 8 orders of magnitude. Thus, virus processes such as entry, disassembly, and egress have generally remained poorly understood. Here we discuss photothermal heterodyne imaging (PHI) as a possible alternative to fluorescence microscopy in the study of single virus-like nanoparticle (VNP) dynamics, with relevance in particular to virus uncoating. Being based on optical absorption rather than emission, PHI could potentially surpass some of the current limitations associated with fluorescent labels. As proof-of-principle, single VNPs self-assembled from 60 nm DNA-functionalized gold nanoparticles (DNA-Au NPs) encapsulated in a Gag protein shell of the Human immunodeficiency virus (HIV-1) were imaged and their photothermal response compared with DNA-Au NPs. For the first-time, the protein stoichiometry of a single virus-like particle was estimated by a method other than electron microscopy.

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Volume, Surface and Hydration Properties of Proteins

Cited by 3 publications

References 17 publications

Modeling Complex Biological Macromolecules: Reduction of Multibead Models

Modeling Complex Biological Macromolecules: Reduction of Multibead Models

Anhydrous and Hydrated Protein Models Derived from High-Resolution and Low-Resolution Techniques

Photothermal Imaging and Measurement of Protein Shell Stoichiometry of Single HIV-1 Gag Virus-like Nanoparticles

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