Computational Structural Biology

Vlad Cojocaru, PhD

Research focus
We apply state-of-the-art Computational Structural Biology methods such as: (i) Structural Modeling, (ii) Bio-molecular Simulations, (iii) Molecular Docking to investigate biological processes from a physico-chemical perspective. We focus on those processes involved in the establishment and maintenance of stem cell pluripotency but we also investigate mechanistically-related processes. Among the topics we are currently studying:

1. DNA recognition by transcription factors involved in the combinatorial control of transcription
2. Cooperativity between transcription factors during DNA recognition
3. Transcription factor folding and its impact on DNA recognition

In addition, we are involved in other projects focused on protein-nucleic acids interactions, protein-membrane interactions and computer-aided drug discovery.

Funding
Financial support: Max Planck Society, DFG SPP1356 Priority Program
Computer resources: Max Planck Society, The PRACE EU intiative

News

Publications

2018

Öztürk MA, Cojocaru V, Wade RC (2018). Towards an ensemble view of the linker histone - nucleosome complex structure: A paradigm shift from one to many. Structure, In press

Öztürk MA, Cojocaru V, Wade RC (2018). Dependence of chromatosome structure on linker histone sequence and post-translational modifications. Biophys J., In press

Wang C, Srivastava Y, Jankowski A, Malik V, Wei Y, del Rosario R, Cojocaru V, Prabhakar S, Jauch R (2018). DNA mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1. Nucleic Acids Res., doi: 10.1093/nar/gky259

2017

Hu C, Malik V, Chang YK, Veerapandian V  Srivastava Y, Huang YH, Hou L, Cojocaru V, Stormo GD, Jauch R. Coop-Seq Analysis Demonstrates that Sox2 Evokes Latent Specificities in the DNA Recognition by Pax6. J Mol Biol. 2017 Oct 16. pii: S0022-2836(17)30495-3. doi: 10.1016/j.jmb.2017.10.013

Jerabek S, Ng CKL, Wu G, Arauzo-Bravo MJ, Kim KP, Esch D, Malik V, Chen Y, Velychko S, Yang X, Cojocaru V, Schöler HR and Jauch R (2017). Changing POU dimerization preferences converts Oct6 into a pluripotency inducer. EMBO Reports, 18(2):319-333

2016

Öztürk M, Pachov G, Wade RC, and Cojocaru V (2016). Conformational selection and dynamic adaptation upon linker histone binding to the nucleosome. Nucleic Acids Research, published online June 7, 2016, doi: 10.1093/nar/gkw514

2015

Yu X, Nandekar P, Mustafa G, Cojocaru V, Lepesheva GI, Wade RC (2015). Ligand tunnels in t. brucei and human CYP51: Insights for parasite-specific drug design. Biochimica Biophysica Acta 1:67-78

Tapia N, MacCarthy C, Esch D, Marthaler AG, Tiermann U, Arauzo-Bravo MJ, De Miguel MP, Jauch R, Cojocaru V, and Schöler HR (2015). Dissecting the role of distinct OCT4-SOX2 heterodimer configurations in pluripotency. Scientific Reports 5:13533

Merino F, Bouvier B, Cojocaru V (2015). Cooperative DNA recognition modulated by an interplay between protein-protein interactions and DNA-mediated allostery. PLoS Computational Biology 11(6): e1004287.

Yu X, Cojocaru V, Mustafa G, Salo-Ahen OM, Lepesheva GI, Wade RC (2015). Dynamics of CYP51: implications for function and inhibitor design. Journal of Molecular Recognition 28(2):59-73.

Narasimhan K, Pillay S, Huang YH, Jayabal S, Udayasuryan B, Veerapandian V, Kolatkar P, Cojocaru V, Pervushin K, Jauch R (2015). DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors. Nucleic Acids Research 43(3):1513-28

2014

Merino F, Ng CKL, Veerapandian V, Schöler HR, Jauch R, Cojocaru V (2014). Structural basis for the SOX-dependent genomic redistribution of OCT4 in stem cell differentiation. Structure 22(9):1274-86

Jerabek S, Merino F, Schöler HR, Cojocaru V (2014). OCT4: dynamic DNA binding pioneers stem cell pluripotency. Biochimica Biophysica Acta 1839(3):138-54

2013

Esch D, Vahokoski J, Groves MR, Pogenberg V, Cojocaru V, Vom Bruch H, Han D, Drexler HC, Araúzo-Bravo MJ, Ng CK, Jauch R, Wilmanns M, Schöler HR (2013). A unique Oct4 interface is crucial for reprogramming to pluripotency. Nature Cell Biology 15(3):295-301

Yu X, Cojocaru V, Wade RC (2013). Conformational Diversity and Ligand Tunnels of Mammalian Cytochrome P450s. Biotechnology and Applied Biochemistry 60(1):134-45

Feldman-Salit A, Hering S, Messiha HL, Veith N, Cojocaru V, Sieg A, Westerhoff HV, Kreikemeyer B, Wade RC, Fiedler T (2013). Regulation of the activity of lactate dehydrogenases from four lactic acid bacteria. Journal of Biological Chemistry 288(29):21295-306

Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013). Organism-adapted specificity of the allosteric regulation of pyruvate kinase in lactic acid bacteria. PLoS Computational Biology 9(7):e1003159

2012

Tapia N, Reinhardt P, Duemmler A, Wu G, Araúzo-Bravo MJ, Esch D, Greber B, Cojocaru V, Rascon CA, Tazaki A, Kump K, Voss R, Tanaka EM, Schöler HR (2012). Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins. Nature Communications 3:1279

Cojocaru V, Winn PJ, Wade RC (2012). Multiple, ligand-dependent routes from the active site of cytochrome P50 2C9. Current Drug Metabolism 13(2):143-154 (invited research article, first and co-corresponding author)3:1279

2011

Cojocaru V, Balali-Mood K, Sansom MS, Wade RC (2011). Structure and dynamics of the membrane-bound cytochrome P450 2C9. PLoS Computational Biology 7(8):e1002152. (journal cover selected to represent this work)

2009

Slanchev K, Stebler J, Goudarzi M, Cojocaru V, Weidinger G, Raz E (2009). Control of Dead end localization and activity-implications for the function of the protein in antagonizing miRNA function.Mechanisms of Development 126:270-277

2007

Cojocaru V, Winn PJ, Wade RC (2007) The ins and outs of cytochrome P450s. Biochimica et Biophysica Acta 770(3):390-401. (journal cover selected to represent this work)

2005

Cojocaru V, Klement R, Jovin TM (2005). Loss of G-A base pairs is insufficient for achieving a large opening of U4 snRNA K-turn motif.Nucleic Acids Research 33:3435-3446. (journal cover selected to represent this work)

Cojocaru V, Nottrott S, Klement R, Jovin TM (2005). The snRNP 15.5K protein folds its cognate K-turn RNA: A combined theoretical and biochemical study. RNA 11:197-209

2004

Stebler J, Spieler D, Slanchev K, Molyneaux KA, Richter U, Cojocaru V, Tarabykin V, Wylie C, Kessel M, Raz E (2004). Primordial germ cell migration in the chick and mouse embryo: the role of the chemokine SDF-1/CXCL12. Developmental Biology 272:351-61