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biophysics
27 downloads
107 views

We have collected computed barrier heights and reaction energies (and associated model structures) for five enzymes from studies published by Himo and co-workers. Using this data, obtained at the B3LYP/6- 311+G(2d,2p)[LANL2DZ]//B3LYP/6-31G(d,p) level of theory,...

["Biophysics","Computational Biology"]
doi:10.7287/peerj.preprints.1741v1
10 downloads
39 views

Here we question the generality of the conventional definition of a native conformation –as the 3-dimensional conformation of an entire globular polypeptide molecule. Although considered common knowledge, and thus not explicitly stated in modern writings, this...

["Biochemistry","Bioengineering","Biophysics","Biotechnology","Molecular Biology"]
doi:10.7287/peerj.preprints.1735v1
42 downloads
251 views

Background. Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate...

["Biophysics"]
doi:10.7717/peerj.1676
65 downloads
243 views

Background/objectives. This study examines the surface activity, resistance to biophysical inhibition, and pulmonary efficacy of a synthetic lung surfactant containing glycerophospholipids combined with Super Mini-B (S-MB) DATK, a novel and stable molecular mimic...

["Bioengineering","Biophysics","Respiratory Medicine"]
doi:10.7717/peerj.1528
80 downloads
384 views

Differential Scanning Calorimetry (DSC) of intact Escherichia coli (E. coli) was used to identify non-lipidic targets of the antimicrobial peptide (AMP) MSI-78. The DSC thermograms revealed that, in addition to its known lytic properties, MSI-78 also has a striking...

["Biophysics","Infectious Diseases"]
doi:10.7717/peerj.1516
124 downloads
826 views

The calcitic lenses in the eyes of Palaeozoic trilobites are unique in the animal kingdom, although the use of calcite would have conveyed great advantages for vision in aquatic systems. Calcite lenses are transparent, and due to their high refractive index they...

["Biophysics","Paleontology"]
doi:10.7717/peerj.1492
74 downloads
572 views

Embryonic cell division is a mechanical process which is predominantly driven by contraction of the cleavage furrow and response of the remaining cellular matter. While most previous studies focused on contractile ring mechanisms of cytokinesis, effects of environmental...

["Biophysics","Cell Biology","Computational Biology","Developmental Biology"]
doi:10.7717/peerj.1490
108 downloads
251 views

The calcitic lenses in the eyes of Palaeozoic trilobites are unique in the animal kingdom, although the use of calcite would have conveyed great advantages for vision in aquatic systems. Calcite lenses are transparent, and due to their high refractive index they...

["Biophysics","Paleontology"]
doi:10.7287/peerj.preprints.1288v2
123 downloads
726 views

In biological mass spectrometry, crude instrumental data need to be converted into meaningful theoretical models. Several data processing and data evaluation steps are required to come to the final results. These operations are often difficult to reproduce, because...

["Bioinformatics","Biophysics","Computational Biology","Mathematical Biology","Statistics"]
doi:10.7717/peerj.1401
83 downloads
481 views

Cholesterol has important functions in the organization of membrane structure and this may be mediated via the formation of cholesterol-rich, liquid-ordered membrane microdomains often referred to as lipid rafts. Methyl-beta-cyclodextrin (cyclodextrin) is commonly...

["Biophysics","Cell Biology","Mathematical Biology"]
doi:10.7717/peerj.1351
47 downloads
73 views

Contrarily to the majority of the members of the lipocalin family, which are stable monomers with the specific OBP fold (a β-barrel consisting of a 8-stranded anti-parallel β-sheet followed by a short α-helical segment, a ninth β-strand, and a disordered C-terminal...

["Biochemistry","Biophysics","Molecular Biology"]
doi:10.7287/peerj.preprints.1454v1
22 downloads
70 views

In a family of monomeric odorant-binding proteins (OBPs), bovine OBP (bOBP), that lacks conserved disulfide bond found in other OBPs, occupies unique niche because of its ability to form domain-swapped dimers. In this study, we analyzed conformational stabilities...

["Biochemistry","Bioinformatics","Biophysics","Molecular Biology"]
doi:10.7287/peerj.preprints.1452v1
31 downloads
100 views

Bovine odorant-binding protein (bOBP) differs from other lipocalins by lacking the conserved disulfide bond and being able to form the domain-swapped dimers. To identify structural features responsible for the formation of the bOBP unique dimeric structure and...

["Biochemistry","Biophysics","Molecular Biology"]
doi:10.7287/peerj.preprints.1445v1
82 downloads
449 views

We present ProCS15: a program that computes the isotropic chemical shielding values of backbone and Cβ atoms given a protein structure in less than a second. ProCS15 is based on around 2.35 million OPBE/6-31G(d,p)//PM6 calculations on tripeptides and small structural...

["Biophysics","Computational Biology"]
doi:10.7717/peerj.1344
126 downloads
846 views

The vibrating reed frequency meter, originally employed by Békésy and later by Wilson as a cochlear model, uses a set of tuned reeds to represent the cochlea’s graded bank of resonant elements and an elastic band threaded between them to provide nearest-neighbour...

["Biophysics","Computational Biology","Mathematical Biology","Otorhinolaryngology","Computational Science"]
doi:10.7717/peerj.1333

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