31 research outputs found
MEPSAnd: Minimum Energy Path Surface Analysis over n-dimensional surfaces.
Summary: Understanding biophysical phenomena from the approach of molecular simulation is becoming
the state-of-art in many research and technology development fields. Energy surfaces with more than
3 dimensions (2 coordinates and energy) are now computationally accessible, yet interpreting the
information they offer is not straightforward and the tasks involved very time-consuming. Here we present
MEPSAnd, an open source GUI-based program that natively calculates minimum energy paths across
energy surfaces of an arbitrary number of dimensions. In addition to the multidimensional analysis of
path through lowest barriers, MEPSAnd can also automatically calculate a finite series of suboptimal
paths. To allow the efficient interpretation of results, MEPSAnd offers three distinct plotting solutions: i)
energy profiles, ii) coordinate projections and iii) network projections. GUI-independent pipelines are also
supported via direct python scripting. Therefore, MEPSAnd is a powerful user friendly tool that streamlines
path-finding tasks on n-dimensional energy surfaces.pre-print1996 K
De novo heterozygous mutations in SMC3 cause a range of cornelia de lange syndrome-overlapping phenotypes
© 2015 WILEY PERIODICALS, INC. Cornelia de Lange syndrome (CdLS) is characterized by facial dysmorphism, growth failure, intellectual disability, limb malformations, and multiple organ involvement. Mutations in five genes, encoding subunits of the cohesin complex (SMC1A, SMC3, RAD21) and its regulators (NIPBL, HDAC8), account for at least 70% of patients with CdLS or CdLS-like phenotypes. To date, only the clinical features from a single CdLS patient with SMC3 mutation has been published. Here, we report the efforts of an international research and clinical collaboration to provide clinical comparison of 16 patients with CdLS-like features caused by mutations in SMC3. Modeling of the mutation effects on protein structure suggests a dominant-negative effect on the multimeric cohesin complex. When compared with typical CdLS, many SMC3-associated phenotypes are also characterized by postnatal microcephaly but with a less distinctive craniofacial appearance, a milder prenatal growth retardation that worsens in childhood, few congenital heart defects, and an absence of limb deficiencies. While most mutations are unique, two unrelated affected individuals shared the same mutation but presented with different phenotypes. This work confirms that de novo SMC3 mutations account for ~1%-2% of CdLS-like phenotypes. Cornelia de Lange syndrome (CdLS) is a multisystem developmental disorder caused by mutation in five genes encoding subunits or regulators of the cohesin complex. To date, only the clinical features of the unique mildly affected CdLS male with SMC3 mutation have been published. Here, we report a series of 16 probands with 15 different intragenic mutations in SMC3 that provide a significant advance in our understanding of the clinical and molecular basis of Cornelia de Lange syndrome and overlapping phenotypes.CdLS Foundation of UK and Ireland for their long-term help and support. M.A.D. and I.D.K. are indebted to the USA Cornelia de Lange Syndrome FoundationPeer Reviewe
MEPSA: Minimum energy pathway analysis for energy landscapes
From conformational studies to atomistic descriptions of enzymatic reactions, potential and free energy landscapes can be used to describe biomolecular systems in detail. However, extracting the relevant data of complex 3D energy surfaces can sometimes be laborious. In this article, we present MEPSA (Minimum Energy Path Surface Analysis), a cross-platform user friendly tool for the analysis of energy landscapes from a transition state theory perspective. Some of its most relevant features are: identification of all the barriers and minima of the landscape at once, description of maxima edge profiles, detection of the lowest energy path connecting two minima and generation of transition state theory diagrams along these paths. In addition to a built-in plotting system, MEPSA can save most of the generated data into easily parseable text files, allowing more versatile uses of MEPSA's output such as the generation of molecular dynamics restraints from a calculated path.Grant IPT2011-0964-900000 (Government of Spain).Peer Reviewe
A novel RAD21 p.(Gln592del) variant expands the clinical description of Cornelia de Lange syndrome type 4 – Review of the literature.
Cornelia de Lange syndrome (CdLS) is a heterogeneous developmental disorder where 70%
of clinically diagnosed patients harbor a mutation in one of five CdLS associated cohesin
proteins. Around 500 mutations have been identified to cause CdLS, however only eight
different alterations are identified in RAD21, encoding the RAD21 cohesin protein that
constitute the link between SMC1A and SMC3 within the cohesin ring. We report a 15-
month-old boy presenting with developmental delay, distinct CdLS facial features,
gastrointestinal reflux in early infancy, testis retention fetal pads and diaphragmatic hernia.
Exome sequencing revealed a novel RAD21 variant, c.1774_1776del; p.(Gln592del),
suggestive of CdLS type 4. Segregation analysis of the two healthy parents confirmed the
variant as de novo and bioinformatic analysis predicted the variant as disease-causing.
Functional assessment by in silico structural model predicted that the p.Gln592del variant
results in a discontinued contact between RAD21-Lys591 and the SMC1A residues Glu1191
and Glu1192, causing changes in the RAD21-SMC1A interface. In conclusion, we report a
novel RAD21 p.(Glu592del) variant that expands the clinical description of CdLS type 4 and
validate the pathogenicity of the variant by in silico structural modeling that displayed
disturbed RAD21-SMC1A interface.pre-print2,82 M
Pathogenic convergence of CNVs in genes functionally associated to a severe neuromotor developmental delay syndrome.
Background
Complex developmental encephalopathy syndromes might be the consequence of unknown genetic alterations that are likely to contribute to the full neurological phenotype as a consequence of pathogenic gene combinations.
Methods
To identify the additional genetic contribution to the neurological phenotype, we studied as a test case a boy, with a KCNQ2 exon-7 partial duplication, by single-nucleotide polymorphism (SNP) microarray to detect copy-number variations (CNVs).
Results
The proband presented a cerebral palsy like syndrome with a severe motor and developmental encephalopathy. The SNP array analysis detected in the proband several de novo CNVs, nine partial gene losses (LRRC55, PCDH9, NALCN, RYR3, ELAVL2, CDH13, ATP1A2, SLC17A5, ANO3), and two partial gene duplications (PCDH19, EFNA5). The biological functions of these genes are associated with ion channels such as calcium, chloride, sodium, and potassium with several membrane proteins implicated in neural cell-cell interactions, synaptic transmission, and axon guidance. Pathogenically, these functions can be associated to cerebral palsy, seizures, dystonia, epileptic crisis, and motor neuron dysfunction, all present in the patient.
Conclusions
Severe motor and developmental encephalopathy syndromes of unknown origin can be the result of a phenotypic convergence by combination of several genetic alterations in genes whose physiological function contributes to the neurological pathogenic mechanism.post-print783 K
Human Mitochondrial HMG-CoA Synthase Deficiency: Role of Enzyme Dimerization Surface and Characterization of Three New Patients.
Mitochondrial 3-hydroxy-3-methylglutaryl-CoA synthase deficiency (mitochondrial
HMG-CoA synthase deficiency or mHS deficiency, OMIM #605911) is an inborn error of metabolism
that affects ketone body synthesis. Acute episodes include vomiting, lethargy, hepatomegaly,
hypoglycemia and dicarboxylic aciduria. The diagnosis is difficult due to the relatively unspecific
clinical and biochemical presentation, and fewer than 30 patients have been described. This work
describes three new patients with mHS deficiency and two missense mutations c.334C>T (p.R112W)
and c.430G>T (p.V144L) previously not reported. We developed a new method to express and
measure the activity of the enzyme and in this work the study is extended to ten new missense
variants including those of our patients. Enzymatic assays showed that three of the mutant proteins
retained some but seven completely lacked activity. The identification of a patient homozygous for
a mutation that retains 70% of enzyme activity opens the door to a new interpretation of the disease
by demonstrating that a modest impairment of enzyme function can actually produce symptoms.
This is also the first study employing molecular dynamics modelling of the enzyme mutations. We
show that the correct maintenance of the dimerization surface is crucial for retaining the structure of
the active center and therefore the activity of the enzyme.post-print1746 K
VRK1 (Y213H) homozygous mutant impairs Cajal bodies in a hereditary case of distal motor neuropathy.
Background: Distal motor neuropathies with a genetic origin have a heterogeneous
clinical presentation with overlapping features affecting distal nerves and
including spinal muscular atrophies and amyotrophic lateral sclerosis. This
indicates that their genetic background is heterogeneous. Patient and methods:
In this work, we have identified and characterized the genetic and molecular
base of a patient with a distal sensorimotor neuropathy of unknown origin. For
this study, we performed whole-exome sequencing, molecular modelling, cloning
and expression of mutant gene, and biochemical and cell biology analysis of
the mutant protein. Results: A novel homozygous recessive mutation in the
human VRK1 gene, coding for a chromatin kinase, causing a substitution
(c.637T > C; p.Tyr213His) in exon 8, was detected in a patient presenting since
childhood a progressive distal sensorimotor neuropathy and spinal muscular
atrophy syndrome, with normal intellectual development. Molecular modelling
predicted this mutant VRK1 has altered the kinase activation loop by disrupting
its interaction with the C-terminal regulatory region. The p.Y213H mutant protein
has a reduced kinase activity with different substrates, including histones
H3 and H2AX, proteins involved in DNA damage responses, such as p53 and
53BP1, and coilin, the scaffold for Cajal bodies. The mutant VRK1(Y213H)
protein is unable to rescue the formation of Cajal bodies assembled on coilin,
in the absence of wild-type VRK1. Conclusion: The VRK1(Y213H) mutant protein
alters the activation loop, impairs the kinase activity of VRK1 causing a
functional insufficiency that impairs the formation of Cajal bodies assembled
on coilin, a protein that regulates SMN1 and Cajal body formation.post-print2120 K
Diversity of mechanisms to control bacterial GTP homeostasis by the mutually exclusive binding of adenine and guanine nucleotides to IMP dehydrogenase.
IMP dehydrogenase(IMPDH) is an essential enzyme that catalyzes the rate-limiting step in the guanine nucleotide pathway. In eukaryotic cells, GTP binding to the regulatory domain allosterically controls the activity of IMPDH by a mechanism that is fine-tuned by post-translational modifications and enzyme polymerization. Nonetheless, the mechanisms of regulation of IMPDH in bacterial cells remain unclear. Using biochemical, structural, and evolutionary analyses, we demonstrate that, in most bacterial phyla, (p)ppGpp compete with ATP to allosterically modulate IMPDH activity by binding to a, previously unrecognized, conserved high affinity pocket within the regulatory domain. This pocket was lost during the evolution of Proteobacteria, making their IMPDHs insensitive to these alarmones. Instead, most proteobacterial IMPDHs evolved to be directly modulated by the balance between ATP and GTP that compete for the same allosteric binding site. Altogether, we demonstrate that the activity of bacterial IMPDHs is allosterically modulated by a universally conserved nucleotide-controlled conformational switch that has divergently evolved to adapt to the specific particularities of each organism. These results reconcile the reported data on the crosstalk between (p)ppGpp signaling and the guanine nucleotide biosynthetic pathway and reinforce the essential role of IMPDH allosteric regulation on bacterial GTP homeostasis.post-print540 K
Two-step ATP-driven opening of cohesin head.
The cohesin ring is a protein complex composed of four core subunits: Smc1A, Smc3, Rad21 and
Stag1/2. It is involved in chromosome segregation, DNA repair, chromatin organization and
transcription regulation. Opening of the ring occurs at the “head” structure, formed of the ATPase
domains of Smc1A and Smc3 and Rad21. We investigate the mechanisms of the cohesin ring opening
using techniques of free molecular dynamics (MD), steered MD and quantum mechanics/molecular
mechanics MD (QM/MM MD). The study allows the thorough analysis of the opening events at the
atomic scale: i) ATP hydrolysis at the Smc1A site, evaluating the role of the carboxy-terminal domain
of Rad21 in the process; ii) the activation of the Smc3 site potentially mediated by the movement of
specific amino acids; and iii) opening of the head domains after the two ATP hydrolysis events. Our
study suggests that the cohesin ring opening is triggered by a sequential activation of the ATP sites
in which ATP hydrolysis at the Smc1A site induces ATPase activity at the Smc3 site. Our analysis also
provides an explanation for the effect of pathogenic variants related to cohesinopathies and cancer.post-print4709 K
Things are not always what they seem: From Cornelia de Lange to KBG phenotype in a girl with genetic variants in NIPBL and ANKRD11.
post-print509 K