Salem Faham

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University of North Carolina at Chapel Hill

Institute for Geological and Geochemical Research, Research Centre for Astronomy and Earth Sciences, Hungarian Academy of Sciences

Huilong Hou

University of Maryland, College Park

niha ansari

Gujarat Technological University

Suresh G S Giriyapur

Sugarcane Breeding Institute (Indian Council of Agricultural Research)

Gerhard Fischer

University of Cambridge

Md Arifuzzaman

Hajee Mohammad Danesh Science & Technolgy University, Bangladesh

Angelos Kanellis

Aristotle University of Thessaloniki

Amar Joshi

University of Oxford

Nacer Abouchi

CPE Lyon

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Papers by Salem Faham

Protein Rethreading

Biophysical Journal, 2016

Substrate binding to the multidrug transporter MepA

Biochimica Et Biophysica Acta Biomembranes, Jun 23, 2014

Detergent concentration determines which substrate binds more tightly to MepA.The hydrophobic sub... more Detergent concentration determines which substrate binds more tightly to MepA.The hydrophobic substrates interact directly with detergent micelles.The inactive D183A mutant binds more weakly to substrates.TPP inhibits substrate binding to MepA.MepA is a multidrug transporter from Staphylococcus aureus that confers multidrug resistance through the efflux of a wide array of hydrophobic substrates. To evaluate the ability of MepA to recognize different substrates, the dissociation constants for interactions between MepA and three of its substrates (acriflavine (Acr), rhodamine 6G (R6G), and ethidium (Et)) were measured. Given that MepA is purified in the presence of detergents and that its substrates are hydrophobic, we examined the effect of the detergent concentration on the dissociation constant. We demonstrate that all three substrates interact directly with the detergent micelles. Additionally, we find the detergent effect on the KD value to be highly substrate-dependent. The KD value for R6G is greatly influenced by the detergent, whereas the KD values for Acr and Et are only modestly affected. The effect of the inactive D183A mutant on binding was also evaluated. The D183A mutant shows lower affinity toward Acr and Et.

Bicelles Coming of Age

Methods in Enzymology, 2015

Biological membranes represent a unique environment in which integral membrane proteins (MPs) fol... more Biological membranes represent a unique environment in which integral membrane proteins (MPs) fold to perform diverse biological functions. In many cases, lipids support the native conformation or mediate important interactions between MPs. It is therefore imperative to develop methods that maintain this support for the structural and functional analyses of an exceedingly important class of biological macromolecules. Bicelles are detergent-stabilized phospholipid bilayer discs into which MPs can be reconstituted for biophysical studies. Here, we review recent advances and emerging concepts in employing bicelles for the crystallization and structure determination of MPs. We discuss variations of established procedures as well as alternative approaches, and we present a summary and analysis of the conditions used for bicelle-mediated MP crystallization.

Substrate binding to the multidrug transporter MepA

Biochimica et biophysica acta, 2014

MepA is a multidrug transporter from Staphylococcus aureus that confers multidrug resistance thro... more MepA is a multidrug transporter from Staphylococcus aureus that confers multidrug resistance through the efflux of a wide array of hydrophobic substrates. To evaluate the ability of MepA to recognize different substrates, the dissociation constants for interactions between MepA and three of its substrates (acriflavine (Acr), rhodamine 6G (R6G), and ethidium (Et)) were measured. Given that MepA is purified in the presence of detergents and that its substrates are hydrophobic, we examined the effect of the detergent concentration on the dissociation constant. We demonstrate that all three substrates interact directly with the detergent micelles. Additionally, we find the detergent effect on the KD value to be highly substrate-dependent. The KD value for R6G is greatly influenced by the detergent, whereas the KD values for Acr and Et are only modestly affected. The effect of the inactive D183A mutant on binding was also evaluated. The D183A mutant shows lower affinity toward Acr and Et.

Three-Dimensional Structures of Acidic and Basic Fibroblast Growth Factors

Science, 1991

Members of the fibroblast growth factor (FGF) family of proteins stimulate the proliferation and ... more Members of the fibroblast growth factor (FGF) family of proteins stimulate the proliferation and differentiation of a variety of cell types through receptor-mediated pathways. The three-dimensional structures of two members of this family, bovine acidic FGF and human basic FGF, have been crystallographically determined. These structures contain 12 antiparallel beta strands organized into a folding pattern with approximate threefold internal

Native interface of the SAM domain polymer of TEL

BMC structural biology, Jan 22, 2002

TEL is a transcriptional repressor containing a SAM domain that forms a helical polymer. In a num... more TEL is a transcriptional repressor containing a SAM domain that forms a helical polymer. In a number of hematologic malignancies, chromosomal translocations lead to aberrant fusions of TEL-SAM to a variety of other proteins, including many tyrosine kinases. TEL-SAM polymerization results in constitutive activation of the tyrosine kinase domains to which it becomes fused, leading to cell transformation. Thus, inhibitors of TEL-SAM self-association could abrogate transformation in these cells. In previous work, we determined the structure of a mutant TEL-SAM polymer bearing a Val to Glu substitution in center of the subunit interface. It remained unclear how much the mutation affected the architecture of the polymer, however. Here we determine the structure of the native polymer interface. To accomplish this goal, we introduced mutations that block polymer extension, producing a heterodimer with a wild-type interface. We find that the structure of the wild-type polymer interface is qu...

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Structural characterization of MepB from Staphylococcus aureus reveals homology to endonucleases

Protein Science, 2014

The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance.... more The MepRAB operon in Staphylococcus aureus has been identified to play a role in drug resistance. Although the functions of MepA and MepR are known, little information is available on the function of MepB. Here we report the X-ray structure of MepB to 2.1 Å revealing its structural similarity to the PD-(D/E)XK family of endonucleases. We further show that MepB binds DNA and RNA, with a higher affinity towards RNA and single stranded DNA than towards double stranded DNA. Notably, the PD-(D/E)XK catalytic active site residues are not conserved in MepB. MepB&amp;amp;amp;amp;amp;amp;#39;s association with a drug resistance operon suggests that it plays a role in responding to antimicrobials. This role is likely carried out through MepB&amp;amp;amp;amp;amp;amp;#39;s interactions with nucleic acids.

Monomeric Structure of the Human EphB2 Sterile a Motif Domain

The sterile a motif (SAM) domain is a protein module found in many diverse signaling proteins. SA... more The sterile a motif (SAM) domain is a protein module found in many diverse signaling proteins. SAM domains in some systems have been shown to self-associate. Pre- vious crystal structures of an EphA4-SAM domain dimer (Stapleton, D., Balan, I., Pawson, T., and Sicheri, F. (1999) Nat. Struct. Biol. 6, 44 - 49) and a possible EphB2- SAM oligomer (Thanos, C. D., Goodwill, K. E., and Bowie, J. U. (1999) Science 283, 833- 836) both revealed large interfaces comprising an exchange of N-terminal pep- tide arms. Within the arm, a conserved hydrophobic residue (Tyr-8 in the EphB2-SAM structure or Phe-910 in the EphA4-SAM structure) is anchored into a hydropho- bic cleft on a neighboring molecule. Here we have solved a new crystal form of the human EphB2-SAM domain that has the same overall SAM domain fold yet has no substantial intermolecular contacts. In the new struc- ture, the N-terminal peptide arm of the EphB2-SAM do- main protrudes out from the core of the molecule, leav- ing both the a...

Monomeric Structure of the Human EphB2 Sterile alpha Motif Domain

Journal of Biological Chemistry, 1999

The sterile ␣ motif (SAM) domain is a protein module found in many diverse signaling proteins. SA... more The sterile ␣ motif (SAM) domain is a protein module found in many diverse signaling proteins. SAM domains in some systems have been shown to self-associate. Previous crystal structures of an EphA4-SAM domain dimer (Stapleton, D., Balan, I., Pawson, T., and Sicheri, F. (1999) Nat. Struct. Biol. 6, 44 -49) and a possible EphB2-SAM oligomer (Thanos, C. D., Goodwill, K. E., and Bowie, J. U. (1999) Science 283, 833-836) both revealed large interfaces comprising an exchange of N-terminal peptide arms. Within the arm, a conserved hydrophobic residue (Tyr-8 in the EphB2-SAM structure or Phe-910 in the EphA4-SAM structure) is anchored into a hydrophobic cleft on a neighboring molecule.

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How to Prepare Membrane Proteins for Solid-State NMR: A Case Study on the α-Helical Integral Membrane Protein Diacylglycerol Kinase fromE. coli

by Salem Faham and J. Mason

Chembiochem, 2005

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Crystal structure of the murine Voltage Dependent Anion Channel 1 (mVDAC1) at 2.3 A resolution

The Faseb Journal, Apr 1, 2009

A C ¿ H...O Hydrogen Bond in a Membrane Protein Is Not Stabilizing

Journal of the American Chemical Society Jacs, 2004

A Cα-H...O hydrogen bond in a membrane protein is not stabilizing

Journal of the American Chemical Society, 2004

Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calcula... more

A C a -H��O Hydrogen Bond in a Membrane Protein Is Not Stabilizing

J Am Chem Soc, 2004

The crystal structure of mouse VDAC1 at 2.3 Ã resolution reveals mechanistic insights into metabolite gating

Pnas, 2009

The voltage-dependent anion channel (VDAC) constitutes the major pathway for the entry and exit o... more The voltage-dependent anion channel (VDAC) constitutes the major pathway for the entry and exit of metabolites across the outer membrane of the mitochondria and can serve as a scaffold for molecules that modulate the organelle. We report the crystal structure of a beta-barrel eukaryotic membrane protein, the murine VDAC1 (mVDAC1) at 2.3 Å resolution, revealing a high-resolution image of its

A C alpha-H...O hydrogen bond in a membrane protein is not stabilizing

Journal of the American Chemical Society, Jan 3, 2004

Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calcula... more Hydrogen bonds involving a carbon donor are very common in protein structures, and energy calculations suggest that Calpha-H...O hydrogen bonds could be about one-half the strength of traditional hydrogen bonds. It has therefore been proposed that these nontraditional hydrogen bonds could be a significant factor in stabilizing proteins, particularly membrane proteins as there is a low dielectric and no competition from water in the bilayer core. Nevertheless, this proposition has never been tested experimentally. Here, we report an experimental test of the significance of Calpha-H...O bonds for protein stability. Thr24 in bacteriorhodopsin, which makes an interhelical Calpha-H...O hydrogen bond to the Calpha of Ala51, was changed to Ala, Val, and Ser, and the thermodynamic stability of the mutants was measured. None of the mutants had significantly reduced stability. In fact, T24A was more stable than the wild-type protein by 0.6 kcal/mol. Crystal structures were determined for each...

Construction of helix-bundle membrane proteins

Advances in Protein Chemistry, 2003

... CONSTRUCTION OF HELIX-BUNDLE MEMBRANE PROTEINS By AARON K. CHAMBERLAIN,SALEM FAHAM, SARAH YOH... more

Chapter 5 Practical Aspects of Membrane Proteins Crystallization in Bicelles

Current Topics in Membranes, 2009

An Architectural Framework That May Lie at the Core of the Postsynaptic Density

Science, 2006

The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic... more The postsynaptic density (PSD) is a complex assembly of proteins associated with the postsynaptic membrane that organizes neurotransmitter receptors, signaling pathways, and regulatory elements within a cytoskeletal matrix. Here we show that the sterile alpha motif domain of rat Shank3/ProSAP2, a master scaffolding protein located deep within the PSD, can form large sheets composed of helical fibers stacked side by side. Zn2+, which is found in high concentrations in the PSD, binds tightly to Shank3 and may regulate assembly. Sheets of the Shank protein could form a platform for the construction of the PSD complex.