scholarly journals Aromatic π-networks in Sm/LSm protein interfaces

2014 ◽  
Vol 12 (1) ◽  
pp. 27-39
Author(s):  
Luka Breberina ◽  
Milan Nikolic ◽  
Srdjan Stojanovic
Keyword(s):  
Solvent Accessibility ◽  
Frequency Of Occurrence ◽  
Stabilization Centers ◽  
Protein Interfaces ◽  
Accessibility Pattern

In this work, we have analyzed the influence of ?-? interactions on stability and properties of Sm/LSm assemblies. Phe residues were found to be involved in ?-? interactions much more frequently than Tyr or His. Similarly, the Phe-Phe ?-? interacting pair had the highest frequency of occurrence. Furthermore, a significant number of ?-networks were observed at the interface of Sm/LSm proteins. Generally speaking, the distance between the interacting pairs was in the range of 5-6 ?. 3? and 7?-networks were found to frequently have plane-plane angles less than 60?. Solvent accessibility pattern of Sm/LSm proteins revealed that all of the interacting residues were from buried areas. Moreover, most of the ?-? interacting residues of Sm/LSm proteins were evolutionary conserved and were in the strand regions. A high percentage of these residues could be considered as stabilization centers that (significantly) contribute to the net stability of Sm/LSm proteins.

scholarly journals APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility

2010 ◽  
Vol 11 (1) ◽  
pp. 174 ◽  
Author(s):  
Jun-Feng Xia ◽  
Xing-Ming Zhao ◽  
Jiangning Song ◽  
De-Shuang Huang
Keyword(s):  
Hot Spots ◽  
Solvent Accessibility ◽  
Accurate Prediction ◽  
Protein Interfaces

scholarly journals SPServer: split-statistical potentials for the analysis of protein structures and protein–protein interactions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Joaquim Aguirre-Plans ◽  
Alberto Meseguer ◽  
Ruben Molina-Fernandez ◽  
Manuel Alejandro Marín-López ◽  
Gaurav Jumde ◽  
...  
Keyword(s):  
Amino Acid ◽  
Solvent Accessibility ◽  
Protein Structures ◽  
Web Server ◽  
Protein Docking ◽  
Scoring Functions ◽  
Statistical Potentials ◽  
Protein Folds ◽  
Protein Interfaces

Abstract Background Statistical potentials, also named knowledge-based potentials, are scoring functions derived from empirical data that can be used to evaluate the quality of protein folds and protein–protein interaction (PPI) structures. In previous works we decomposed the statistical potentials in different terms, named Split-Statistical Potentials, accounting for the type of amino acid pairs, their hydrophobicity, solvent accessibility and type of secondary structure. These potentials have been successfully used to identify near-native structures in protein structure prediction, rank protein docking poses, and predict PPI binding affinities. Results Here, we present the SPServer, a web server that applies the Split-Statistical Potentials to analyze protein folds and protein interfaces. SPServer provides global scores as well as residue/residue-pair profiles presented as score plots and maps. This level of detail allows users to: (1) identify potentially problematic regions on protein structures; (2) identify disrupting amino acid pairs in protein interfaces; and (3) compare and analyze the quality of tertiary and quaternary structural models. Conclusions While there are many web servers that provide scoring functions to assess the quality of either protein folds or PPI structures, SPServer integrates both aspects in a unique easy-to-use web server. Moreover, the server permits to locally assess the quality of the structures and interfaces at a residue level and provides tools to compare the local assessment between structures. Server address https://sbi.upf.edu/spserver/.

Measurement of Solvent Accessibility at Protein–Protein Interfaces

2005 ◽  
pp. 065-080 ◽  
Author(s):  
Jeffrey G. Mandell ◽  
Abel Baerga-Ortiz ◽  
Arnold M. Falick ◽  
Elizabeth A. Komives
Keyword(s):  
Solvent Accessibility ◽  
Protein Interfaces

TEM studies of tweed microstructures in annealed amelia albite

1990 ◽  
Vol 48 (4) ◽  
pp. 1064-1065
Author(s):  
Y. J. Kim ◽  
D. M. Henderson
Keyword(s):  
Annealing Time ◽  
The Other ◽  
Frequency Of Occurrence ◽  
Systematic Trend ◽  
Tweed Structure

Natural Amelia albite (Ab99.3An0.1Or0.6) annealed at 1073° and 924°C for various periods up to 140 days has been studied by NMR. TEM studies of the same sample revealed a distinct tweed microstructure in some samples annealed at both 1073°C and 924°C. On the whole, the quasi-regular tweed has a periodicity of 100 - 200 Å in both directions, one nearly normal to b* and the other approximately parallel to b*, which gives rise to two-directional streaking in SADP’s (Fig. 1 and 2). However, there are some differences in the tweed structure developed on annealing at 1073°C and at 924°C in albite.Albite samples annealed at 1073° show a systematic trend in their development of tweed structures: the regularity, periodicity, and frequency of occurrence increase with annealing time during the first 3 days, and then decrease gradually until no tweed microstructures are seen in samples annealed for more than 15 days. The tweed structure proceeds locally to form one-directional twin-like microstructures.

An Investigation of the Assumptions Underlying the Scoring System of the Arizona Articulation Proficiency Scale: Revised

1979 ◽  
Vol 10 (4) ◽  
pp. 241-245
Author(s):  
Richard J. Schissel ◽  
Linda B. James
Keyword(s):  
Scoring System ◽  
Frequency Of Occurrence

This study examines the assumptions underlying the scoring system of the Arizona Articulation Proficiency Scale: Revised. Twenty-one children between the ages of four years two months and six years 11 months were administered the Arizona Articulation Proficiency Scale: Revised and the Screening Deep Test of Articulation. The subjects' performance on the two tests was compared for the phones: [s], [l], [r], [t∫], [θ], [∫], [k], [f], and [t]. Results suggested that 1) the production of most sounds in only two contexts does not necessarily reflect the accuracy of production of those sounds in other contexts, and 2) for the sounds tested, the weightings assigned on the basis of their frequency of occurrence rather than the frequency with which they were misarticulated overestimated the extent of many articulation errors.

Teachers' Stereotypes of Children Who Wear Hearing Aids

1981 ◽  
Vol 12 (3) ◽  
pp. 139-144 ◽  
Author(s):  
Cletus G. Fisher ◽  
Kenneth Brooks
Keyword(s):  
Elementary School ◽  
School Child ◽  
Hearing Aids ◽  
Hearing Aid ◽  
Social Implications ◽  
Elementary School Child ◽  
Classroom Teachers ◽  
Frequency Of Occurrence ◽  
Service Training

Classroom teachers were asked to list the traits they felt were characteristic of the elementary school child who wears a hearing aid. These listings were evaluated according to the desirability of the traits and were studied regarding frequency of occurrence, desirability, and educational, emotional, and social implications. The results of the groupings are discussed in terms of pre-service and in-service training.

Direct coding for frequency of occurrence

1991 ◽  
Author(s):  
Iohn Jonides ◽  
Caren M. Jones
Keyword(s):  
Frequency Of Occurrence

Computerization of the Patient History -Patient Answers Compared with Medical Records

1986 ◽  
Vol 25 (04) ◽  
pp. 222-228 ◽  
Author(s):  
M. J. Quaak ◽  
R. F. Westerman ◽  
J. A. Schouten ◽  
A. Hasman ◽  
J. H. Bemmel
Keyword(s):  
Internal Medicine ◽  
Medical Records ◽  
Patient Record ◽  
Frequency Of Occurrence ◽  
History Taking ◽  
Patient History ◽  
Patient Complaints ◽  
Computerized Patient Record ◽  
Extensive Information ◽  
Experienced Physician

SummaryComputerized medical history taking, in which patients answer questions by using a terminal, is compared with the written medical record for a group of 99 patients in internal medicine. Patient complaints were analysed with respect to their frequency of occurrence for all important tracts, such as the respiratory, the gastro-intestinal and the uro-genital tracts. About 36% of over 3,200 patient answers were identical in the patient record and the written record, but a considerable percentage of complaints (56%), that were present in the patient record, were missing in the written record; the reverse was true for 4.5%. A computerized patient record appears to contain more extensive information about patient complaints, still to be interpreted by the experienced physician.

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