Nicholas P Schafer
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Explore the profile of Nicholas P Schafer including associated specialties, affiliations and a list of published articles.
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50
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975
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Recent Articles
1.
Jaafari H, Bueno C, Schafer N, Martin J, Morcos F, Wolynes P
Proc Natl Acad Sci U S A
. 2024 May;
121(21):e2322428121.
PMID: 38739795
Protein evolution is guided by structural, functional, and dynamical constraints ensuring organismal viability. Pseudogenes are genomic sequences identified in many eukaryotes that lack translational activity due to sequence degradation and...
2.
Sahin C, Motso A, Gu X, Feyrer H, Lama D, Arndt T, et al.
J Am Chem Soc
. 2023 May;
145(19):10659-10668.
PMID: 37145883
Liquid-liquid phase separation (LLPS) of heterogeneous ribonucleoproteins (hnRNPs) drives the formation of membraneless organelles, but structural information about their assembled states is still lacking. Here, we address this challenge through...
3.
Gu X, Schafer N, Bueno C, Lu W, Wolynes P
PLoS Comput Biol
. 2022 Nov;
18(11):e1010657.
PMID: 36346822
A prion-like RNA-binding protein, CPEB3, can regulate local translation in dendritic spines. CPEB3 monomers repress translation, whereas CPEB3 aggregates activate translation of its target mRNAs. However, the CPEB3 aggregates, as...
4.
Lin X, George J, Schafer N, Chau K, Birnbaum M, Clementi C, et al.
Nat Comput Sci
. 2022 Sep;
1(5):362-373.
PMID: 36090450
Accurate assessment of TCR-antigen specificity at the whole immune repertoire level lies at the heart of improved cancer immunotherapy, but predictive models capable of high-throughput assessment of TCR-peptide pairs are...
5.
Bueno C, Liman J, Schafer N, Cheung M, Wolynes P
PLoS Comput Biol
. 2022 May;
18(5):e1010105.
PMID: 35533192
Actin networks are essential for living cells to move, reproduce, and sense their environments. The dynamic and rheological behavior of actin networks is modulated by actin-binding proteins such as α-actinin,...
6.
Guzovsky A, Schafer N, Wolynes P, Ferreiro D
Methods Mol Biol
. 2021 Nov;
2376:387-398.
PMID: 34845622
We present a detailed heuristic method to quantify the degree of local energetic frustration manifested by protein molecules. Current applications are realized in computational experiments where a protein structure is...
7.
Gu X, Schafer N, Wolynes P
Proc Natl Acad Sci U S A
. 2021 Nov;
118(47).
PMID: 34795061
Translation of messenger RNA (mRNA) is regulated through a diverse set of RNA-binding proteins. A significant fraction of RNA-binding proteins contains prion-like domains which form functional prions. This raises the...
8.
Xu Y, Knapp K, LE K, Schafer N, Safari M, Davtyan A, et al.
Proc Natl Acad Sci U S A
. 2021 Sep;
118(38).
PMID: 34518234
Amyloid fibrillization is an exceedingly complex process in which incoming peptide chains bind to the fibril while concertedly folding. The coupling between folding and binding is not fully understood. We...
9.
Cys-labeling kinetics of membrane protein GlpG: a role for specific SDS binding and micelle changes?
Otzen D, Pedersen J, Somavarapu A, Clement A, Ji M, Petersen E, et al.
Biophys J
. 2021 Aug;
120(18):4115-4128.
PMID: 34370995
Empirically, α-helical membrane protein folding stability in surfactant micelles can be tuned by varying the mole fraction MF of anionic (sodium dodecyl sulfate (SDS)) relative to nonionic (e.g., dodecyl maltoside...
10.
Lu W, Bueno C, Schafer N, Moller J, Jin S, Chen X, et al.
PLoS Comput Biol
. 2021 Feb;
17(2):e1008308.
PMID: 33577557
We present OpenAWSEM and Open3SPN2, new cross-compatible implementations of coarse-grained models for protein (AWSEM) and DNA (3SPN2) molecular dynamics simulations within the OpenMM framework. These new implementations retain the chemical...