Directional structural features of globular proteins

The efficacy of the particle beam LC/FT-IR interface, in its development as a tool for the determination of dynamic protein structure from experiments such as HPLC separations and folding/refolding intermediate analysis, is presented here. The particle beam apparatus can be used to desolvate proteins rapidly in preparation of IR measurements. Several experiments have been designed to determine whether the operation of the particle beam apparatus causes alteration to the complex structural features of globular proteins, and whether it produces a solid-state spectrum representative of protein solution structure. It is shown here that the structural integrity of β-lactoglobulin is maintained when nebulized, desolvated from solution, and deposited onto the IR-substrate. Since enzyme activity is dependent upon the maintenance of higher-order structure, a complementary series of spectrophotometric-activity experiments with lysozyme collected from the particle beam were performed to determine the state of the tertiary and quaternary structures. The lysozyme particle beam deposit not only produced a secondary structure estimate similar to that of solution; it also retained its biological activity. It is demonstrated that the particle beam can induce structural changes in proteins with a carrier-liquid concentration gradient; this characteristic is useful for band assignment.

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Could network structures generated with simple rules imposed on a cubic lattice reproduce the structural descriptors of globular proteins?

10.1101/2020.10.01.321992 ◽

2020 ◽

Cited By ~ 1

Author(s):

Osman Burak Okan ◽

Deniz Turgut ◽

Canan Atilgan ◽

Ali Rana Atilgan ◽

Rahmi Ozisik

Keyword(s):

Rational Design ◽

Structural Characteristics ◽

Orientational Order ◽

Sphere Packing ◽

Careful Analysis ◽

Globular Proteins ◽

Structural Features ◽

Coarse Grained ◽

Topological Descriptors ◽

Bond Orientational Order

AbstractA direct way to spot structural features that are universally shared among proteins is to find proper analogues from simpler condensed matter systems. In most cases, sphere-packing arguments provide a straightforward route for structural comparison, as they successfully characterize a wide array of materials such as close packed crystals, dense liquids, and structural glasses. In the current study, the feasibility of creating ensembles of artificial structures that can automatically reproduce a large number of geometrical and topological descriptors of globular proteins is investigated. Towards this aim, a simple cubic (SC) arrangement is shown to provide the best background lattice after a careful analysis of the residue packing trends from 210 proteins. It is shown that a minimalistic set of ground rules imposed on this lattice is sufficient to generate structures that can mimic real proteins. In the proposed method, 210 such structures are generated by randomly removing residues (beads) from clusters that have a SC lattice arrangement until a predetermined residue concentration is achieved. All generated structures are checked for residue connectivity such that a path exists between any two residues. Two additional sets are prepared from the initial structures via random relaxation and a reverse Monte Carlo simulated annealing (RMC-SA) algorithm, which targets the average radial distribution function (RDF) of 210 globular proteins. The initial and relaxed structures are compared to real proteins via RDF, bond orientational order parameters, and several descriptors of network topology. Based on these features, results indicate that the structures generated with 40% occupancy via the proposed method closely resemble real residue networks. The broad correspondence established this way indicates a non-superficial link between the residue networks and the defect laden cubic crystalline order. The presented approach of identifying a minimalistic set of operations performed on a target lattice such that each resulting cluster possess structural characteristics largely indistinguishable from that of a coarse-grained globular protein opens up new venues in structural characterization, native state recognition, and rational design of proteins.

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Application of proteases in the meat industry: a review

Meat Industry Journal ◽

10.37861/2618-8252-2020-11-32-36 ◽

2020 ◽

pp. 32-36

Author(s):

D.V. Khvostov ◽

◽

E.A. Konorov ◽

M.V. Zakharova ◽

Zh.I. Andreeva-Kovalevskaya ◽

...

Keyword(s):

Connective Tissue ◽

Raw Materials ◽

Globular Proteins ◽

Structural Features ◽

High Potential ◽

Meat Industry ◽

Rigid Structure ◽

Bacterial Origin ◽

Relevant Today ◽

Separate Class

The rigidity of meat systems is due to many factors, including different ratio of fibrillar and globular proteins, as well as their structural features. The need to soften meat systems with a high content of various types of connective tissue, as well as the possibility of correcting the processes associated with abnormal autolysis during the maturation of meat raw materials and the formation of a dry rigid structure, are relevant today. The review presents the use of peptidases of plant, animal and bacterial origin, including their separate class — collagenases, which are used for tenderizing meat. Also, recombinant targeting proteases that have high potential are presented; so, there is a need to develop effective applications for their use.

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TMSNP: a web server to predict pathogenesis of missense mutations in the transmembrane region of membrane proteins

NAR Genomics and Bioinformatics ◽

10.1093/nargab/lqab008 ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Adrián Garcia-Recio ◽

José Carlos Gómez-Tamayo ◽

Iker Reina ◽

Mercedes Campillo ◽

Arnau Cordomí ◽

...

Keyword(s):

Machine Learning ◽

Membrane Proteins ◽

Genome Sequencing ◽

Web Server ◽

Globular Proteins ◽

Structural Features ◽

Missense Mutations ◽

Transmembrane Region ◽

Machine Learning Model ◽

Pathogenic Effects

Abstract The massive amount of data generated from genome sequencing brings tons of newly identified mutations, whose pathogenic/non-pathogenic effects need to be evaluated. This has given rise to several mutation predictor tools that, in general, do not consider the specificities of the various protein groups. We aimed to develop a predictor tool dedicated to membrane proteins, under the premise that their specific structural features and environment would give different responses to mutations compared to globular proteins. For this purpose, we created TMSNP, a database that currently contains information from 2624 pathogenic and 196 705 non-pathogenic reported mutations located in the transmembrane region of membrane proteins. By computing various conservation parameters on these mutations in combination with annotations, we trained a machine-learning model able to classify mutations as pathogenic or not. TMSNP (freely available at http://lmc.uab.es/tmsnp/) improves considerably the prediction power of commonly used mutation predictors trained with globular proteins.

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A STUDY ON SOME STRUCTURAL FEATURES RESPONSIBLE FOR SARS-COV-2 INFECTION FATALITY

10.31219/osf.io/m62ba ◽

2021 ◽

Author(s):

JAYDIP DATTA

Keyword(s):

Molecular Weight ◽

Biological Activities ◽

Globular Proteins ◽

Structural Features ◽

Spike Protein ◽

Radius Of Gyration ◽

Fatality Rate ◽

Hydrodynamic Properties ◽

Standard Curve ◽

Best Fit

In this article Covid19 is structurally analysed to establish the pathogenic attack through its spike protein ( 1 ) The most of the bio -macromolecules starting from globular proteins to viruses with a high molecular weight average showing polymeric nature as to induce their biological activities. The tremendous infectivity mainly depends on one most important hydrodynamic properties like Zigzag nature of viral walk ( 2 ) for a specific molecular weight ( M ). Hydrodynamic s nature of mRNA –viruses like SARS-COV-2 is analysed to compute the random– zigzag motion ( 2,3) of the virus known as Radius of Gyration( Rg ) value of virus . For computation of Rg a standard curve( 4 )of Rg – M is statistically analysed with best fit regression analysis like Morgan – Morgan – Finney ( MMF ) ( 5 ) model . This zigzag – random walk ( 2 ) of SARS-COV-2 molecule computed from Rg value may be considered as fatality rate of infection ( 6 ).

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Structural features that predict real-value fluctuations of globular proteins

Proteins Structure Function and Bioinformatics ◽

10.1002/prot.24040 ◽

2012 ◽

Vol 80 (5) ◽

pp. 1425-1435 ◽

Cited By ~ 15

Author(s):

Michal Jamroz ◽

Andrzej Kolinski ◽

Daisuke Kihara

Keyword(s):

Globular Proteins ◽

Structural Features ◽

Real Value

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The study of conformational states of proteins by nuclear magnetic resonance

Biochemical Journal ◽

10.1042/bj2310001 ◽

1985 ◽

Vol 231 (1) ◽

pp. 1-10 ◽

Cited By ~ 22

Author(s):

I D Campbell ◽

C M Dobson ◽

R J P Williams

Keyword(s):

Conformational Analysis ◽

Small Molecules ◽

Conformational Changes ◽

Globular Proteins ◽

Structural Features ◽

Dynamical Behaviour ◽

Structural Description ◽

Coat Proteins ◽

Virus Coat ◽

Denatured States

By the use of examples, mainly of rather rigid proteins, we hope to have shown that conformational analysis of proteins is a problem that is not simply related to the conformational analysis of small molecules. The primary difficulties with proteins are (1) the multitude of possible conformers, (2) the complex dynamical behaviour and (3) the degree of co-operativity within the molecules. Any experimentally derived structural description of a protein is an attempt to represent some average of a complex time dependence. N.m.r. techniques have now reached the point where it is possible to use them to describe many detailed structural features of small globular proteins in solution and to detect and to describe conformational changes in such proteins. In addition, analysis is becoming possible of much less ordered regions of polypeptides, such as are found in less compact proteins, of for example myosin, histones and virus coat proteins, or in denatured states. The limits to the detailed conformational analysis of such proteins are likely to be ones of reality rather than method but the description of the properties shown in Table 1 is by its very nature an extremely important problem in conformational analysis of dynamic macromolecules.

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Electron microscopy and diffraction studies of polyimides

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074069 ◽

1983 ◽

Vol 41 ◽

pp. 28-29

Author(s):

O.C. de Hodgins ◽

K. R. Lawless ◽

R. Anderson

Keyword(s):

Electron Microscopy ◽

Electron Microscope ◽

Structural Features ◽

Inert Atmosphere ◽

Polyimide Films ◽

Resolution Electron ◽

The Matrix ◽

High Resolution Electron Microscope ◽

Diffraction Patterns ◽

Polymeric Samples

Commercial polyimide films have shown to be homogeneous on a scale of 5 to 200 nm. The observation of Skybond (SKB) 705 and PI5878 was carried out by using a Philips 400, 120 KeV STEM. The objective was to elucidate the structural features of the polymeric samples. The specimens were spun and cured at stepped temperatures in an inert atmosphere and cooled slowly for eight hours. TEM micrographs showed heterogeneities (or nodular structures) generally on a scale of 100 nm for PI5878 and approximately 40 nm for SKB 705, present in large volume fractions of both specimens. See Figures 1 and 2. It is possible that the nodulus observed may be associated with surface effects and the structure of the polymers be regarded as random amorphous arrays. Diffraction patterns of the matrix and the nodular areas showed different amorphous ring patterns in both materials. The specimens were viewed in both bright and dark fields using a high resolution electron microscope which provided magnifications of 100,000X or more on the photographic plates if desired.

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Skeletal elements of crinoid echinoderms: High-resolution structural and microanalytical results

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100074768 ◽

1983 ◽

Vol 41 ◽

pp. 194-195

Author(s):

D. F. Blake ◽

L. F. Allard ◽

D. R. Peacor

Keyword(s):

High Resolution ◽

Marine Invertebrates ◽

Sea Urchins ◽

Structural Features ◽

Sea Stars ◽

High Resolution Tem ◽

Relationship Of ◽

The Relationship ◽

Insight Into

Echinodermata is a phylum of marine invertebrates which has been extant since Cambrian time (c.a. 500 m.y. before the present). Modern examples of echinoderms include sea urchins, sea stars, and sea lilies (crinoids). The endoskeletons of echinoderms are composed of plates or ossicles (Fig. 1) which are with few exceptions, porous, single crystals of high-magnesian calcite. Despite their single crystal nature, fracture surfaces do not exhibit the near-perfect {10.4} cleavage characteristic of inorganic calcite. This paradoxical mix of biogenic and inorganic features has prompted much recent work on echinoderm skeletal crystallography. Furthermore, fossil echinoderm hard parts comprise a volumetrically significant portion of some marine limestones sequences. The ultrastructural and microchemical characterization of modern skeletal material should lend insight into: 1). The nature of the biogenic processes involved, for example, the relationship of Mg heterogeneity to morphological and structural features in modern echinoderm material, and 2). The nature of the diagenetic changes undergone by their ancient, fossilized counterparts. In this study, high resolution TEM (HRTEM), high voltage TEM (HVTEM), and STEM microanalysis are used to characterize tha ultrastructural and microchemical composition of skeletal elements of the modern crinoid Neocrinus blakei.

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Study of the Molecular Architecture of Keratin Filaments by Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100053310 ◽

1982 ◽

Vol 40 ◽

pp. 118-119

Author(s):

U. Aebi ◽

P. Rew ◽

T.-T. Sun

Keyword(s):

Electron Microscopy ◽

Structural Organization ◽

Cell Types ◽

Structural Features ◽

Molecular Architecture ◽

The Past ◽

Keratin Filaments ◽

Different Types ◽

10 Nm Filaments ◽

Different Cell Types

Various types of intermediate-sized (10-nm) filaments have been found and described in many different cell types during the past few years. Despite the differences in the chemical composition among the different types of filaments, they all yield common structural features: they are usually up to several microns long and have a diameter of 7 to 10 nm; there is evidence that they are made of several 2 to 3.5 nm wide protofilaments which are helically wound around each other; the secondary structure of the polypeptides constituting the filaments is rich in ∞-helix. However a detailed description of their structural organization is lacking to date.

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