1
|
Argüello-Miranda O, Marchand AJ, Kennedy T, Russo MAX, Noh J. Cell cycle-independent integration of stress signals by Xbp1 promotes Non-G1/G0 quiescence entry. J Cell Biol 2022; 221:212720. [PMID: 34694336 PMCID: PMC8548912 DOI: 10.1083/jcb.202103171] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 08/27/2021] [Accepted: 10/05/2021] [Indexed: 12/15/2022] Open
Abstract
Cellular quiescence is a nonproliferative state required for cell survival under stress and during development. In most quiescent cells, proliferation is stopped in a reversible state of low Cdk1 kinase activity; in many organisms, however, quiescent states with high-Cdk1 activity can also be established through still uncharacterized stress or developmental mechanisms. Here, we used a microfluidics approach coupled to phenotypic classification by machine learning to identify stress pathways associated with starvation-triggered high-Cdk1 quiescent states in Saccharomyces cerevisiae. We found that low- and high-Cdk1 quiescent states shared a core of stress-associated processes, such as autophagy, protein aggregation, and mitochondrial up-regulation, but differed in the nuclear accumulation of the stress transcription factors Xbp1, Gln3, and Sfp1. The decision between low- or high-Cdk1 quiescence was controlled by cell cycle-independent accumulation of Xbp1, which acted as a time-delayed integrator of the duration of stress stimuli. Our results show how cell cycle-independent stress-activated factors promote cellular quiescence outside G1/G0.
Collapse
Affiliation(s)
- Orlando Argüello-Miranda
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| | - Ashley J Marchand
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Taylor Kennedy
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX.,School of Natural Sciences and Mathematics, University of Texas at Dallas, Richardson, TX
| | - Marielle A X Russo
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX
| | - Jungsik Noh
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX
| |
Collapse
|
2
|
Matos GS, Madeira JB, Fernandes CM, Dasilva D, Masuda CA, Del Poeta M, Montero-Lomelí M. Regulation of sphingolipid synthesis by the G1/S transcription factor Swi4. Biochim Biophys Acta Mol Cell Biol Lipids 2021; 1866:158983. [PMID: 34062255 PMCID: PMC8512607 DOI: 10.1016/j.bbalip.2021.158983] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/19/2021] [Accepted: 05/21/2021] [Indexed: 11/23/2022]
Abstract
SBF (Swi4/Swi6 Binding Factor) complex is a crucial regulator of G1/S transition in Saccharomyces cerevisiae. Here, we show that SBF complex is required for myriocin resistance, an inhibitor of sphingolipid synthesis. This phenotype was not shared with MBF complex mutants nor with deletion of the Swi4p downstream targets, CLN1/CLN2. Based on data mining results, we selected putative Swi4p targets related to sphingolipid metabolism and studied their gene transcription as well as metabolite levels during progression of the cell cycle. Genes which encode key enzymes for the synthesis of long chain bases (LCBs) and ceramides were periodically transcribed during the mitotic cell cycle, having a peak at G1/S, and required SWI4 for full transcription at this stage. In addition, HPLC-MS/MS data indicated that swi4Δ cells have decreased levels of sphingolipids during progression of the cell cycle, particularly, dihydrosphingosine (DHS), C24-phytoceramides and C24-inositolphosphoryl ceramide (IPC) while it had increased levels of mannosylinositol phosphorylceramide (MIPC). Furthermore, we demonstrated that both inhibition of de novo sphingolipid synthesis by myriocin or SWI4 deletion caused partial arrest at the G2/M phase. Importantly, our lipidomic data demonstrated that the sphingolipid profile of WT cells treated with myriocin resembled that of swi4Δ cells, with lower levels of DHS, IPC and higher levels of MIPC. Taken together, these results show that SBF complex plays an essential role in the regulation of sphingolipid homeostasis, which reflects in the correct progression through the G2/M phase of the cell cycle.
Collapse
Affiliation(s)
- Gabriel S Matos
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Juliana B Madeira
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Deveney Dasilva
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA
| | - Claudio A Masuda
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maurizio Del Poeta
- Department of Microbiology and Immunology, Stony Brook University, Stony Brook, NY, USA; Institute of Chemical Biology and Drug Discovery, Stony Brook University, Stony Brook, NY, USA; Veteran Administration Medical Center, Northport, NY, USA; MicroRid Technologies Inc., Dix Hills, NY, USA; Division of Infectious Diseases, School of Medicine, Stony Brook University, NY, USA
| | - Monica Montero-Lomelí
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil.
| |
Collapse
|
3
|
Donovan DA, Crandall JG, Truong VN, Vaaler AL, Bailey TB, Dinwiddie D, Banks OGB, McKnight LE, McKnight JN. Basis of specificity for a conserved and promiscuous chromatin remodeling protein. eLife 2021; 10:e64061. [PMID: 33576335 PMCID: PMC7968928 DOI: 10.7554/elife.64061] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/11/2021] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic genomes are organized dynamically through the repositioning of nucleosomes. Isw2 is an enzyme that has been previously defined as a genome-wide, nonspecific nucleosome spacing factor. Here, we show that Isw2 instead acts as an obligately targeted nucleosome remodeler in vivo through physical interactions with sequence-specific factors. We demonstrate that Isw2-recruiting factors use small and previously uncharacterized epitopes, which direct Isw2 activity through highly conserved acidic residues in the Isw2 accessory protein Itc1. This interaction orients Isw2 on target nucleosomes, allowing for precise nucleosome positioning at targeted loci. Finally, we show that these critical acidic residues have been lost in the Drosophila lineage, potentially explaining the inconsistently characterized function of Isw2-like proteins. Altogether, these data suggest an 'interacting barrier model,' where Isw2 interacts with a sequence-specific factor to accurately and reproducibly position a single, targeted nucleosome to define the precise border of phased chromatin arrays.
Collapse
Affiliation(s)
- Drake A Donovan
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | | | - Vi N Truong
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Abigail L Vaaler
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Thomas B Bailey
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Devin Dinwiddie
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Orion GB Banks
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Laura E McKnight
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Jeffrey N McKnight
- Institute of Molecular Biology, University of OregonEugeneUnited States
- Phil and Penny Knight Campus for Accelerating Scientific Impact, University of OregonEugeneUnited States
| |
Collapse
|
4
|
Zhang Q, Yu Y, Zhang J, Liang H. Using single-index ODEs to study dynamic gene regulatory network. PLoS One 2018; 13:e0192833. [PMID: 29474376 PMCID: PMC5825071 DOI: 10.1371/journal.pone.0192833] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 01/31/2018] [Indexed: 12/18/2022] Open
Abstract
With the development of biotechnology, high-throughput studies on protein-protein, protein-gene, and gene-gene interactions become possible and attract remarkable attention. To explore the interactions in dynamic gene regulatory networks, we propose a single-index ordinary differential equation (ODE) model and develop a variable selection procedure. We employ the smoothly clipped absolute deviation penalty (SCAD) penalized function for variable selection. We analyze a yeast cell cycle gene expression data set to illustrate the usefulness of the single-index ODE model. In real data analysis, we group genes into functional modules using the smoothing spline clustering approach. We estimate state functions and their first derivatives for functional modules using penalized spline-based nonparametric mixed-effects models and the spline method. We substitute the estimates into the single-index ODE models, and then use the penalized profile least-squares procedure to identify network structures among the models. The results indicate that our model fits the data better than linear ODE models and our variable selection procedure identifies the interactions that may be missed by linear ODE models but confirmed in biological studies. In addition, Monte Carlo simulation studies are used to evaluate and compare the methods.
Collapse
Affiliation(s)
- Qi Zhang
- Department of Statistics, Qingdao University, Qingdao, China
| | - Yao Yu
- Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Jun Zhang
- Institute of Statistical Sciences at Shenzhen University, Shenzhen University, Shenzhen, China
| | - Hua Liang
- Department of Statistics, George Washington University, Washington, D.C., United States of America
- * E-mail:
| |
Collapse
|
5
|
Liu J, Huang J, Zhao Y, Liu H, Wang D, Yang J, Zhao W, Taylor IA, Peng YL. Structural basis of DNA recognition by PCG2 reveals a novel DNA binding mode for winged helix-turn-helix domains. Nucleic Acids Res 2014; 43:1231-40. [PMID: 25550425 PMCID: PMC4333399 DOI: 10.1093/nar/gku1351] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The MBP1 family proteins are the DNA binding subunits of MBF cell-cycle transcription factor complexes and contain an N terminal winged helix-turn-helix (wHTH) DNA binding domain (DBD). Although the DNA binding mechanism of MBP1 from Saccharomyces cerevisiae has been extensively studied, the structural framework and the DNA binding mode of other MBP1 family proteins remains to be disclosed. Here, we determined the crystal structure of the DBD of PCG2, the Magnaporthe oryzae orthologue of MBP1, bound to MCB-DNA. The structure revealed that the wing, the 20-loop, helix A and helix B in PCG2-DBD are important elements for DNA binding. Unlike previously characterized wHTH proteins, PCG2-DBD utilizes the wing and helix-B to bind the minor groove and the major groove of the MCB-DNA whilst the 20-loop and helix A interact non-specifically with DNA. Notably, two glutamines Q89 and Q82 within the wing were found to recognize the MCB core CGCG sequence through making hydrogen bond interactions. Further in vitro assays confirmed essential roles of Q89 and Q82 in the DNA binding. These data together indicate that the MBP1 homologue PCG2 employs an unusual mode of binding to target DNA and demonstrate the versatility of wHTH domains.
Collapse
Affiliation(s)
- Junfeng Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Jinguang Huang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China College of Agronomy and Plant Protection, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yanxiang Zhao
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Huaian Liu
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China
| | - Dawei Wang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Jun Yang
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Wensheng Zhao
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Ian A Taylor
- Division of Molecular Structure, MRC-NIMR, London, NW7 1AA, UK
| | - You-Liang Peng
- MOA Key Laboratory of Plant Pathology, China Agricultural University, Beijing 100193, China State key Laboratory of Agrobiotechnology, China Agricultural University, Beijing 100193, China
| |
Collapse
|
6
|
Zhao Y, Su H, Zhou J, Feng H, Zhang KQ, Yang J. The APSES family proteins in fungi: Characterizations, evolution and functions. Fungal Genet Biol 2014; 81:271-80. [PMID: 25534868 DOI: 10.1016/j.fgb.2014.12.003] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2014] [Revised: 12/08/2014] [Accepted: 12/12/2014] [Indexed: 10/24/2022]
Abstract
The APSES protein family belongs to transcriptional factors of the basic helix-loop-helix (bHLH) class, the originally described members (APSES: Asm1p, Phd1p, Sok2p, Efg1p and StuAp) are used to designate this group of proteins, and they have been identified as key regulators of fungal development and other biological processes. APSES proteins share a highly conserved DNA-binding domain (APSES domain) of about 100 amino acids, whose central domain is predicted to form a typical bHLH structure. Besides APSES domain, several APSES proteins also contain additional domains, such as KilA-N and ankyrin repeats. In recent years, an increasing number of APSES proteins have been identified from diverse fungi, and they involve in numerous biological processes, such as sporulation, cellular differentiation, mycelial growth, secondary metabolism and virulence. Most fungi, including Aspergillus fumigatus, Aspergillus nidulans, Candida albicans, Fusarium graminearum, and Neurospora crassa, contain five APSES proteins. However, Cryptococcus neoformans only contains two APSES proteins, and Saccharomyces cerevisiae contains six APSES proteins. The phylogenetic analysis showed the APSES domains from different fungi were grouped into four clades (A, B, C and D), which is consistent with the result of homologous alignment of APSES domains using DNAman. The roles of APSES proteins in clade C have been studied in detail, while little is known about the roles of other APSES proteins in clades A, B and D. In this review, the biochemical properties and functional domains of APSES proteins are predicted and compared, and the phylogenetic relationship among APSES proteins from various fungi are analyzed based on the APSES domains. Moreover, the functions of APSES proteins in different fungi are summarized and discussed.
Collapse
Affiliation(s)
- Yong Zhao
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Hao Su
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Jing Zhou
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Huihua Feng
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Ke-Qin Zhang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China
| | - Jinkui Yang
- Laboratory for Conservation and Utilization of Bio-Resources, Key Laboratory of Microbial Diversity in Southwest China, Ministry of Education, Yunnan University, Kunming 650091, PR China.
| |
Collapse
|
7
|
Abstract
Nearly 20% of the budding yeast genome is transcribed periodically during the cell division cycle. The precise temporal execution of this large transcriptional program is controlled by a large interacting network of transcriptional regulators, kinases, and ubiquitin ligases. Historically, this network has been viewed as a collection of four coregulated gene clusters that are associated with each phase of the cell cycle. Although the broad outlines of these gene clusters were described nearly 20 years ago, new technologies have enabled major advances in our understanding of the genes comprising those clusters, their regulation, and the complex regulatory interplay between clusters. More recently, advances are being made in understanding the roles of chromatin in the control of the transcriptional program. We are also beginning to discover important regulatory interactions between the cell-cycle transcriptional program and other cell-cycle regulatory mechanisms such as checkpoints and metabolic networks. Here we review recent advances and contemporary models of the transcriptional network and consider these models in the context of eukaryotic cell-cycle controls.
Collapse
|
8
|
Weirauch MT, Hughes TR. A catalogue of eukaryotic transcription factor types, their evolutionary origin, and species distribution. Subcell Biochem 2011; 52:25-73. [PMID: 21557078 DOI: 10.1007/978-90-481-9069-0_3] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Transcription factors (TFs) play key roles in the regulation of gene expression by binding in a sequence-specific manner to genomic DNA. In eukaryotes, DNA binding is achieved by a wide range of structural forms and motifs. TFs are typically classified by their DNA-binding domain (DBD) type. In this chapter, we catalogue and survey 91 different TF DBD types in metazoa, plants, fungi, and protists. We briefly discuss well-characterized TF families representing the major DBD superclasses. We also examine the species distributions and inferred evolutionary histories of the various families, and the potential roles played by TF family expansion and dimerization.
Collapse
Affiliation(s)
- Matthew T Weirauch
- Banting and Best Department of Medical Research, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, M5S 3E1, Canada,
| | | |
Collapse
|
9
|
Chernatynskaya AV, Deleeuw L, Trent JO, Brown T, Lane AN. Structural analysis of the DNA target site and its interaction with Mbp1. Org Biomol Chem 2009; 7:4981-91. [PMID: 19907790 DOI: 10.1039/b912309a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The solution structure of a 14 base-pair non-self complementary DNA duplex containing the consensus-binding site of the yeast transcription factor Mbp1 has been determined by NMR using a combination of scalar coupling analysis, time-dependent NOEs, residual dipolar couplings and 13C-edited NMR spectroscopy of a duplex prepared with one strand uniformly labeled with 13C-nucleotides. As expected, the free DNA duplex is within the B-family of structures, and within experimental limits is straight. However, there are clear local structural variations associated with the consensus CGCG element in the binding sequence that are important for sequence recognition. In the complex, the DNA bends around the protein, which also undergoes some conformational rearrangement in the C-terminal region. Structural constraints derived from paramagnetic perturbation experiments with spin-labeled DNA, chemical shift perturbation experiments of the DNA, previous cross-saturation, chemical shift perturbation experiments on the protein, information from mutational analysis, and electrostatics calculations have been used to produce a detailed docked structure using the known solution conformation of the free protein and other spectroscopic information about the Mbp1:DNA complex. A Monte Carlo-based docking procedure with restrained MD in a fully solvated system subjected to available experimental constraints produced models that account for the available structural data, and can rationalize the extensive thermodynamic data about the Mbp1:DNA complex. The protein:DNA interface is closely packed and is associated with a small number of specific contacts. The structure shows an extensive positively charged surface that accounts for the high polyelectrolyte contribution to binding.
Collapse
|
10
|
Deleeuw L, Tchernatynskaia AV, Lane AN. Thermodynamics and Specificity of the Mbp1−DNA Interaction. Biochemistry 2008; 47:6378-85. [DOI: 10.1021/bi702339q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lynn Deleeuw
- J. G. Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
| | - Anna V. Tchernatynskaia
- J. G. Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
| | - Andrew N. Lane
- J. G. Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, and Department of Chemistry, University of Louisville, Louisville, Kentucky 40208
| |
Collapse
|
11
|
McLaughlin WA, Kulp DW, de la Cruz J, Lu XJ, Lawson CL, Berman HM. A structure-based method for identifying DNA-binding proteins and their sites of DNA-interaction. ACTA ACUST UNITED AC 2005; 5:255-65. [PMID: 15704013 DOI: 10.1007/s10969-005-4902-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2004] [Accepted: 11/17/2004] [Indexed: 01/11/2023]
Abstract
A classification model of a DNA-binding protein chain was created based on identification of alpha helices within the chain likely to bind to DNA. Using the model, all chains in the Protein Data Bank were classified. For many of the chains classified with high confidence, previous documentation for DNA-binding was found, yet no sequence homology to the structures used to train the model was detected. The result indicates that the chain model can be used to supplement sequence based methods for annotating the function of DNA-binding. Four new candidates for DNA-binding were found, including two structures solved through structural genomics efforts. For each of the candidate structures, possible sites of DNA-binding are indicated by listing the residue ranges of alpha helices likely to interact with DNA.
Collapse
Affiliation(s)
- William A McLaughlin
- Department of Chemistry and Chemical Biology, Rutgers-The State University of New Jersey, 610 Taylor Road, Piscataway, NJ 08854-8087, USA
| | | | | | | | | | | |
Collapse
|
12
|
Prestegard JH, Mayer KL, Valafar H, Benison GC. Determination of protein backbone structures from residual dipolar couplings. Methods Enzymol 2005; 394:175-209. [PMID: 15808221 PMCID: PMC1808351 DOI: 10.1016/s0076-6879(05)94007-x] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
There are a number of circumstances in which a focus on determination of the backbone structure of a protein, as opposed to a complete all-atom structure, may be appropriate. This is particularly the case for structures determined as a part of a structural genomics initiative in which computational modeling of many sequentially related structures from the backbone of a single family representative is anticipated. It is, however, also the case when the backbone may be a stepping-stone to more targeted studies of ligand interaction or protein-protein interaction. Here an NMR protocol is described that can produce a backbone structure of a protein without the need for extensive experiments directed at side chain resonance assignment or the collection of structural information on side chains. The procedure relies primarily on orientational constraints from residual dipolar couplings as opposed to distance constraints from NOEs. Procedures for sample preparation, data acquisition, and data analysis are described, along with examples from application to small target proteins of a structural genomics project.
Collapse
Affiliation(s)
- J H Prestegard
- Complex Carbohydrate Research Center, University of Georgia, Athens 30602, USA
| | | | | | | |
Collapse
|
13
|
Qu Y, Guo JT, Olman V, Xu Y. Protein structure prediction using sparse dipolar coupling data. Nucleic Acids Res 2004; 32:551-61. [PMID: 14744980 PMCID: PMC373331 DOI: 10.1093/nar/gkh204] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2003] [Revised: 12/10/2003] [Accepted: 12/10/2003] [Indexed: 12/17/2022] Open
Abstract
Residual dipolar coupling (RDC) represents one of the most exciting emerging NMR techniques for protein structure studies. However, solving a protein structure using RDC data alone is still a highly challenging problem. We report here a computer program, RDC-PROSPECT, for protein structure prediction based on a structural homolog or analog of the target protein in the Protein Data Bank (PDB), which best aligns with the (15)N-(1)H RDC data of the protein recorded in a single ordering medium. Since RDC-PROSPECT uses only RDC data and predicted secondary structure information, its performance is virtually independent of sequence similarity between a target protein and its structural homolog/analog, making it applicable to protein targets beyond the scope of current protein threading techniques. We have tested RDC-PROSPECT on all (15)N-(1)H RDC data (representing 43 proteins) deposited in the BioMagResBank (BMRB) database. The program correctly identified structural folds for 83.7% of the target proteins, and achieved an average alignment accuracy of 98.1% residues within a four-residue shift.
Collapse
Affiliation(s)
- Youxing Qu
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | | | | | | |
Collapse
|
14
|
Current awareness on yeast. Yeast 2003; 20:837-44. [PMID: 12886942 DOI: 10.1002/yea.946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|