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article

Function2Form Bridge—Toward synthetic protein holistic performance prediction

Venkata V. B. Yallapragada, Sidney P. Walker, Ciaran Devoy, Stephen Buckley, more

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 462 - 475

Protein engineering and synthetic biology stand to benefit immensely from recent advances in silico tools for structural and functional analyses of proteins. In the context of designing novel proteins, current in silico tools inform the user on individual parameters of a query protein, with output scores/metrics unique to each parameter. In reality, proteins feature multiple “parts”/functions and...

article

Delineation of a new structural motif involving NHN γ‐turn

Jesmita Dhar, Raghuvansh Kishore, Pinak Chakrabarti

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 431 - 439

Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non‐redundant protein chains reveals the existence of a three‐residue, (i − 1) to (i + 1), structural motif, having two hydrogen‐bonded five‐membered pseudo rings (the first, an NH···OC involving the first residue,...

article

Molecular basis of drug resistance in smoothened receptor: An in silico study of protein resistivity and specificity

Noopur Sinha, Saikat Chowdhury, Ram Rup Sarkar

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 514 - 526

Smoothened (SMO) antagonist Vismodegib effectively inhibits the Hedgehog pathway in proliferating cancer cells. In early stage of treatment, Vismodegib exhibited promising outcomes to regress the tumors cells, but ultimately relapsed due to the drug resistive mutations in SMO mostly occurring before (primary mutations G497W) or after (acquired mutations D473H/Y) anti‐SMO therapy. This study investigates...

article

In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4

Yoel Rodríguez, Guillermo Gerona‐Navarro, Roman Osman, Ming‐Ming Zhou

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 414 - 430

Bromodomains (BrDs), a conserved structural module in chromatin‐associated proteins, are well known for recognizing ε‐N‐acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD containing protein (BrD1 and BrD2) that plays a critical role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biological functions; hence...

article

Lysosomal acid lipase does not have a propeptide and should not be considered being a proprotein

Thea B. Strøm, Terje Vinje, Katrine Bjune, Luís T. Costa, more

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 440 - 448

Lysosomal acid lipase (LAL) plays an important role in lipid metabolism by performing hydrolysis of triglycerides and cholesteryl esters in the lysosome. Based upon characteristics of LAL purified from human liver, it has been proposed that LAL is a proprotein with a 55 residue propeptide that may be essential for proper folding, intracellular transport, or enzymatic function. However, the biological...

article

Accessory mutations balance the marginal stability of the HIV‐1 protease in drug resistance

Thomas R. Weikl, Bahram Hemmateenejad

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 476 - 484

The HIV‐1 protease is a major target of inhibitor drugs in AIDS therapies. The therapies are impaired by mutations of the HIV‐1 protease that can lead to resistance to protease inhibitors. These mutations are classified into major mutations, which usually occur first and clearly reduce the susceptibility to protease inhibitors, and minor, accessory mutations that occur later and individually do not...

article

The unusual conformation of cross‐strand disulfide bonds is critical to the stability of β‐hairpin peptides

Evelyne Deplazes, Yanni K.‐Y. Chin, Glenn F. King, Ricardo L. Mancera

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 485 - 502

The cross‐strand disulfides (CSDs) found in β‐hairpin antimicrobial peptides (β‐AMPs) show a unique disulfide geometry that is characterized by unusual torsion angles and a short Cα‐Cα distance. While the sequence and disulfide bond connectivity of disulfide‐rich peptides is well studied, much less is known about the disulfide geometry found in CSDs and their role in the stability of β‐AMPs. To address...

article

Issue Information

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 395 - 396

article

Machine learning techniques for protein function prediction

Rosalin Bonetta, Gianluca Valentino

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 397 - 413

Proteins play important roles in living organisms, and their function is directly linked with their structure. Due to the growing gap between the number of proteins being discovered and their functional characterization (in particular as a result of experimental limitations), reliable prediction of protein function through computational means has become crucial. This paper reviews the machine learning...

article

Having your cake and eating it too: Flexibility and power with mass univariate statistics for ERP data

Eric C. Fields, Gina R. Kuperberg

Psychophysiology > 57 > 2 > n/a - n/a

ERP studies produce large spatiotemporal data sets. These rich data sets are key to enabling us to understand cognitive and neural processes. However, they also present a massive multiple comparisons problem, potentially leading to a large number of studies with false positive effects (a high Type I error rate). Standard approaches to ERP statistical analysis, which average over time windows and regions...

article

Issue Information

Psychophysiology > 57 > 2 > n/a - n/a

article

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

J. Eduardo Fajardo, Rojan Shrestha, Nelson Gil, Adam Belsom, more

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 540 - 540

article

The influence of stimulus valence on perceptual processing of facial expressions and subsequent response inhibition

Laura A. Stockdale, Robert G. Morrison, Rebecca L. Silton

Psychophysiology > 57 > 2 > n/a - n/a

The constant interplay between affective processing and cognitive control supports emotion regulation and appropriate social functioning. Even when affective stimuli are processed implicitly, threat‐related stimuli are prioritized in the earliest stages of processing; yet, it remains unclear how implicit attention to affect influences subsequent cognitive control functions. The present study evaluated...

article

Dysfunctional cognitive control and reward processing in adolescents with Internet gaming disorder

Qi Li, Yong Wang, Zhong Yang, Weine Dai, more

Psychophysiology > 57 > 2 > n/a - n/a

Developmental theories posit that immature cognitive control and excessive reward‐seeking capacities may be a risk factor for addictive behaviors during adolescence, but the control and reward capacities have rarely been assessed experimentally in adolescents with Internet gaming disorder (IGD) simultaneously. This electrophysiological study examined inhibitory control and reward processing in adolescents...

article

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

Ana Damjanovic, Ada Y. Chen, Robert L. Rosenberg, Daniel R. Roe, more

Proteins: Structure, Function, and Bioinformatics > 88 > 3 > 527 - 539

The selectivity filter (SF) of bacterial voltage‐gated sodium channels consists of four glutamate residues arranged in a C₄ symmetry. The protonation state population of this tetrad is unclear. To address this question, we simulate the pore domain of bacterial voltage‐gated sodium channel of Magnetococcus sp. (Na_vMs) through constant pH methodology in explicit solvent and free energy perturbation...

article

Economic growth through entrepreneurship: Determinants of self‐employed income across regional economies

David B. Willis, David W. Hughes, Kathryn A. Boys, Devin C. Swindall

Papers in Regional Science > 99 > 1 > 73 - 95

Knowledge of the determinants of self‐employment income is critical to entrepreneurial development strategies if the development goal is to increase incomes not just employment. Using American Community Survey data, unconditional quantile regression is used to investigate differences in the relationship between entrepreneurial income and an array of individual, industry, and regional characteristics...

article

Related to what? Reviewing the literature on technological relatedness: Where we are now and where can we go?

Adam Whittle, Dieter F. Kogler

Papers in Regional Science > 99 > 1 > 97 - 113

The objective of this paper is to critically review contemporary insights derived from studies that focus on relatedness. A well‐established body of literature has identified three approaches for measuring relatedness, those based on co‐occurrence matrices, industrial hierarchy and resource similarity. From these measures, several authors have begun developing relational networks to capture the branching...

article

Factors influencing farmers' intentions for urban–rural harmony in metropolitan fringes and regional differences therein

Wei Cao, Shenglu Zhou, Shaohua Wu, Chaoye Song

Papers in Regional Science > 99 > 1 > 201 - 224

Farmers' intentions is the intrinsic motivation of the urban–rural harmony development. However, there are few reports examining the factors influencing farmers' intentions. Based on the household questionnaire survey in Pukou district of Nanjing City, the main driving factors to farmers' intentions in metropolitan fringes of China and regional differences therein were quantitatively analysed. The...

article

Inter‐regional networks and productive efficiency in Japan

Akihiro Otsuka

Papers in Regional Science > 99 > 1 > 115 - 133

Traditional agglomeration theories cannot explain Japan's sustained reduction of regional disparities. This study employs stochastic frontier analysis to investigate the role of inter‐regional networks in improving productive efficiency using the concept of “borrowed size.” Improved inter‐regional networks are a driving force for strengthening local economies and converging regional disparities. Borrowed...

article

Are functional regions more homogeneous than administrative regions? A test using hierarchical linear models

Alexandra Wicht, Per Kropp, Barbara Schwengler

Papers in Regional Science > 99 > 1 > 135 - 164

We investigate whether economic functional regions capture spatial clustering of core economic indicators better than administrative regions. For this purpose, we use hierarchical linear models to measure the degree of homogenization of different regional delineations. Our results for Germany show that economic functional regions tend to capture spatial clustering better than administrative ones....

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Search results

Function2Form Bridge—Toward synthetic protein holistic performance prediction

Delineation of a new structural motif involving NHN γ‐turn

Molecular basis of drug resistance in smoothened receptor: An in silico study of protein resistivity and specificity

In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4

Lysosomal acid lipase does not have a propeptide and should not be considered being a proprotein

Accessory mutations balance the marginal stability of the HIV‐1 protease in drug resistance

The unusual conformation of cross‐strand disulfide bonds is critical to the stability of β‐hairpin peptides

Issue Information

Machine learning techniques for protein function prediction

Having your cake and eating it too: Flexibility and power with mass univariate statistics for ERP data

Issue Information

Assessment of chemical‐crosslink‐assisted protein structure modeling in CASP13

The influence of stimulus valence on perceptual processing of facial expressions and subsequent response inhibition

Dysfunctional cognitive control and reward processing in adolescents with Internet gaming disorder

Protonation state of the selectivity filter of bacterial voltage‐gated sodium channels is modulated by ions

Economic growth through entrepreneurship: Determinants of self‐employed income across regional economies

Related to what? Reviewing the literature on technological relatedness: Where we are now and where can we go?

Factors influencing farmers' intentions for urban–rural harmony in metropolitan fringes and regional differences therein

Inter‐regional networks and productive efficiency in Japan

Are functional regions more homogeneous than administrative regions? A test using hierarchical linear models

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